Ras inhibitory peptides and uses thereof

ABSTRACT

The present invention provides peptides comprising a sequence of X- 6 X- 5 X- 4 X- 3 X- 2 X- 1 X 1 PX 3 X 4 PX 6 X 7 PGX 10 X 11 AX 13 X 14 X 15 X 16 LX 18 X 19 X 20 X 21 X 22 X 23 LX 25 X 26 YLX 29 X 30 X 31 X 32  wherein the amino acids X- 6 , X- 5 , X- 4 , X- 3 , X- 2 , X- 1 , X 1 , X 3 , X 4 , X 6 , X 7 , X 10 , X 11 , X 13 , X 14 , X 15 , X 16 , X 18 , X 19 , X 20 , X 21 , X 22 , X 25 , X 26 , X 29 , X 30 , X 31 , and X 32  are as defined herein. The present invention further provides pharmaceutical compositions comprising the peptides and methods of using the peptides for treating proliferative diseases such as cancer which are associated with Ras. Also provided are methods of screening a library of peptide dimers using a peptide dimer display technology.

RELATED APPLICATIONS

This application is a Continuation of U.S. patent application Ser. No.16/696,027, which is a Continuation of U.S. patent application Ser. No.15/312,958, filed Nov. 21, 2016, which is a U.S. National Stage ofPCT/US2015/031961, filed May 21, 2015, which claims the benefit of U.S.Provisional Application No. 62/001,587, filed May 21, 2014. The entireteachings of the above applications are incorporated herein byreference.

Government Support

This invention was made with government support under GM007598 awardedby the National Institutes of Health [NTH]. The government has certainrights in the invention.

REFERENCE TO A SEQUENCE LISTING

This application contains a Sequence Listing in computer readable form.The computer readable form is incorporated herein by reference. SaidASCII copy, created on Sep. 20, 2021, is named 085298 000131 SL.txt andis 66,277 bytes in size.

BACKGROUND OF THE INVENTION

Conventional therapeutics can be broadly divided into two classes: smallmolecules and biologics. Small molecules typically have a mass of <1000Da and bind with high affinity to hydrophobic pockets in proteins, andmany are capable of penetrating cells. Biologics are biomolecules,usually proteins (such as antibodies or hormones) that can bind thesurfaces of other biomolecules with high affinity and specificity, butare unable to efficiently enter cells. It has been estimated that only˜12% of human proteins contain a hydrophobic pocket capable of bindingsmall molecules with high affinity, and that less than 10% of humanproteins are secreted (i.e., transported outside of the cell). As thesetwo groups are not mutually exclusive, more than 78% of human proteinsare therefore inside the cell but lack a hydrophobic binding pocket.These proteins, along with others that are intracellular and containintractable hydrophobic pockets, are often referred to as “undruggable.”Therefore, there remains a need for the development and characterizationof molecules that inhibit the interactions of protein targets.

SUMMARY OF THE INVENTION

While advances have been made in understanding the molecular causes ofhuman disease, the ability to exploit these discoveries for therapeuticbenefit is frequently limited by the inability to make drugs that targetthe processes responsible. Many diseases can be linked to the aberrantactivity of proteins, and while the development of inhibitors forenzymes and extracellular targets is often feasible, these proteinsaccount for only a small fraction of all the proteins in cells. Theremaining proteins are, in most cases, considered therapeuticallyintractable and are sometimes referred to as “undruggable.” The currentinvention solves the problem by providing peptides as described hereinto inhibit the interactions of protein targets and for applications inmethods and systems for screening peptide libraries for inhibiting theinteractions of protein targets.

Many proteins, particularly in higher organisms, carry out theiractivity in part through interactions with other proteins andbiomolecules. The ability to specifically disrupt these interactionscould have great therapeutic benefit, as it may provide a means oftargeting otherwise intractable processes. Therefore, there is a needfor the development and characterization of molecules that inhibit theinteractions of protein targets, such as Ras, which is linked to boththe initiation and progression of a wide array of human cancers. Otherprotein targets include, but are not limited to, the Myc/Maxheterodimer, RalA protein, Beta catenin, YAP/TEAD, and NEMO/IκB kinase.Through high-throughput screening, coupled with directed evolution andrational peptide design using crystal structures, small proteins(sometimes refered to as miniproteins) that bind various proteintargets, including Ras, Myc/Max, RalA, Beta catenin, YAP/TEAD, andNEMO/IκB kinase, and block their ability to engage the effector proteinsnecessary for its oncogenic activity have been identified. The peptidesdescribed herein are useful for the treatment of proliferative diseaesessuch as cancer and other diseases such as rasopathies.

The peptides provided herein are based on mutants of the pancreaticpolypeptide family. In one aspect, provided herein are peptidescomprising a sequence:X₁PX₃X₄PX₆X₇PGDX₁₁AX₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA (SEQ IDNO: 96), wherein the amino acids X₁, X₃, X₄, X₆, X₇, X₁₁, X₁₃, X₁₄, X₁₅,X₁₈, X₁₉, X₂₁, X₂₂, X₂₅, X₂₆, X₂₉, and X₃₀ are as defined herein, andpeptides at least 93% identical to SEQ ID NO: 1 or 96.

In another aspect, provided herein are peptide dimers comprising a firstpeptide associated with a second peptide, wherein the first and secondpeptides each independently comprise a peptide of SEQ ID NO: 1 or 96.The peptide dimers comprise peptide monomers which dimerize in ahead-to-tail arrangement. The peptide dimers can be homodimers orheterodimers.

In one aspect, provided herein are peptides comprising a sequence:X₁PX₃X₄PX₆X₇PGX₁₀X₁₁AX₁₃X₁₄X₁₅DLX₁₈X₁₉X₂₀X₂₁X₂₂X₂₃LX₂₅X₂₆YLX₂₉X₃₀VA (SEQID NO: 12), wherein the amino acids X₁, X₃, X₄, X₆, X₇, X₁₀, X₁₁, X₁₃,X₁₄, X₁₅, X₁₈, X₁₉, X₂₀, X₂₁, X₂₂, X₂₃, X₂₅, X₂₆, X₂₉, and X₃₀ are asdefined herein, and peptides at least 93% identical to SEQ ID NO: 12.

In another aspect, provided herein are peptide dimers comprising a firstpeptide associated with a second peptide, wherein the first and secondpeptides each independently comprise a peptide of SEQ ID NO: 12. Thepeptide dimers comprise peptide monomers which dimerize in ahead-to-tail arrangement. The peptide dimers can be homodimers orheterodimers.

In one aspect, provided herein are peptides comprising a sequence:X-₆X-₅X-₄X-₃X-₂X-₁X₁PX₃X₄PX₆X₇ PGX₁₀ X₁₁AX₁₃X₁₄X₁₅X₁₆LX₁₈X₁₉X₂₀X₂₁X₂₂X₂₃LX₂₅X₂₆YLX₂₉X₃₀X₃₁X₃₂ (SEQ ID NO: 13),wherein the amino acids X-₆, X-₅, X-₄, X-₃, X-₂, X-₁, X₁, X₃, X₄, X₆,X₇, X₁₀, X₁₁, X₁₃, X₁₄, X₁₅, X₁₆, X₁₈, X₁₉, X₂₀, X₂₁, X₂₂, X₂₅, X₂₆,X₂₉, X₃₀, X₃₁, and X₃₂ are as defined herein, and peptides at least 93%identical to SEQ ID NO: 13. In some embodiments, if X-₆ is present, thenX-₆ is Gly and X-₅ to X₁ are present; if X-₅ is present, then X-₅ is Cysor Sec and X-₄ to X₁ are present; if X-₄ is present, then X-₄ is Gly andX-₃ to X₁ are present; if X-₃ is present, then X-₃ is Gly and X-₂ to X₁are present; if X-₂ is present, then X-₂ is Pro, Cys, Sec, or Gly andX-₁ and X₁ are present; if X-₁ is present, then X-₁ is Arg or Gly and X₁is present; and if X₁ is present, X₁ is Gly, Arg, or an amino acidcapable of cross-linking the peptide with another peptide (SEQ ID NO:97). In other embodiments, X-₆ to X₁ are not present (SEQ ID NO: 98).

In another aspect, provided herein are peptide dimers comprising a firstpeptide associated with a second peptide, wherein the first and secondpeptides each independently comprise a peptide of SEQ ID NO: 13. Thepeptide dimers comprise peptide monomers which dimerize in ahead-to-tail arrangement. The peptide dimers can be homodimers orheterodimers.

In one aspect, provided herein are peptides comprising a sequence:X₁PX₃X₄PX₆X₇ PGX₁₀AAX₁₃X₁₄AALHAYX₂₁AX₂₃LX₂₅NYLX₂₉X₃₀VX₃₂ (SEQ ID NO:48), wherein the amino acids X₁, X₃, X₄, X₆, X₇, X₁₀, X₁₃, X₁₄, X₂₁,X₂₃, X₂₅, X₂₉, X₃₀, and X₃₂ are as defined herein, and peptides at least93% identical to SEQ ID NO: 48.

In another aspect, provided herein are peptide dimers comprising a firstpeptide associated with a second peptide, wherein the first and secondpeptides each independently comprise a peptide of SEQ ID NO: 48. Thepeptide dimers comprise peptide monomers which dimerize in ahead-to-tail arrangement. The peptide dimers can be homodimers orheterodimers.

In another aspect, provided herein are peptides comprising aoligomerization domain comprising a sequence: PX_(a)X_(b)PX_(c)X_(d)P(SEQ ID NO: 2), wherein each of X_(a), X_(b), and X_(c) is independentlyany non-proline amino acid, and X_(d) is an amino acid capable ofcross-linking the peptide with another peptide (e.g., cysteine,selenocysteine). The oligomerization domain allows the peptide toassociate with another peptide to form a dimer.

In certain embodiments, peptides comprising a oligomerization domaincomprising a sequence: PX_(a)X_(b)PX_(c)X_(d)P (SEQ ID NO: 2), whereineach of X_(a) and X_(b) is independently any non-proline amino acid, andeach of X_(c) and X_(d) is independently any non-proline amino acid oran amino acid capable of cross-linking the peptide with another peptide(e.g., cysteine, selenocysteine, Phe, Trp, Tyr, or amino acid comprisingan acrylamide moiety such as Dap- and Dab-conjugated acrylamideresidues).

The peptide further comprises an alpha-helical domain comprising asequence: X₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA (SEQ ID NO: 3),wherein X₁₃, X₁₄, X₁₅, X₁₈, X₁₉, X₂₁, X₂₂, X₂₅, X₂₆, X₂₉, and X₃₀are asdefined herein. The alpha-helical domain is involved withprotein-protein interactions and associates with the target protein(e.g., Ras, Myc/Max, RalA, Beta catenin, YAP/TEAD, and NEMO/IκB kinase).

In another aspect, provided herein are peptides comprising analpha-helical domain comprising a sequence:X₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA (SEQ ID NO: 3), wherein X₁₃,X₁₄, X₁₅, X₁₈, X₁₉, X₂₁, X₂₂, X₂₅, X₂₆, X₂₉, and X₃₀are as definedherein.

Exemplary peptides of SEQ ID NO: 1 or 96, 12, and 13 include, but arenot limited to

(SEQ ID NO: 4) GPRRPRCPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 5)GPRRPRCPGDDASIEDLHEYWARLWNYLYRVA, (SEQ ID NO: 6)GRRPRRPRCPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 7)GPRRPRYPGDDAPVEDLIRFYNDLQQYLNVVA, (SEQ ID NO: 8)GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 9)GCGGPRRPRYPGDDACEEDLHEYWARLWNYLYAVA, (SEQ ID NO: 10) GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYRVA, or (SEQ ID NO: 11)GCGGPRRPRRPRYPGDDASIEDLHEYWARLWNYLYAVA.The peptides may comprise a sequence that is about 80% to about 99%homologous to the amino acid sequence of SEQ ID NO: 1 or 96 or SEQ IDNO: 4-11. The peptides may comprise a sequence that is about 80% toabout 99% identical to the amino acid sequence of SEQ ID NO: 1 or 96 orSEQ ID NO: 4-11. The peptides may comprise a sequence that that containsthe amino acid sequence of SEQ ID NO: 1 or 96 or SEQ ID NO: 4-11 with 1,2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid changes (e.g., amino aciddeletions and/or additions). Any of the exemplary peptides and peptidesthat are at least 80% homologous or identical to the exemplary peptidescan form heterodimers or homodimers with one another.

Exemplary peptides of SEQ ID NO: 12, 13, and 48 include, but are notlimited to

(SEQ ID NO: 14) PRRPRCPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 15)PRRPRCPGDDASIEDLHEYWARLWNYLYRVA, (SEQ ID NO: 16)RRPRRPRCPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 17)PRRPRYPGDDAPVEDLIRFYNDLQQYLNVVA, (SEQ ID NO: 18)PRRPRYPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 19)CGGPRRPRYPGDDACEEDLHEYWARLWNYLYAVA, (SEQ ID NO: 20)PRRPRYPGDDASIEDLHEYWARLWNYLYRVA, (SEQ ID NO: 21)PRRPRRPRYPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 22)PRRPRCPGDDASLEDLHEYWARLWNYLYRVA, (SEQ ID NO: 23)PRRPRCPGDQASLEELHEYWARLWNYLYRVA, (SEQ ID NO: 24)PRRPRCPGDNASIKQLHAYWNRLYAYLAAVA, (SEQ ID NO: 25)PRRPRCPGDDASIEDLHEYWQRLYAYLAAVA, (SEQ ID NO: 26)PRRPRCPGDNASIKQLHAYWQRLYAYLAAVA, (SEQ ID NO: 27)PRRPRCPGDNASIRQLHAYWQRLYAYLAAVA, (SEQ ID NO: 28)GCGGPRRPRYPGDAASIAALHAYWARLWNYLYRVA, (SEQ ID NO: 29)PRRPRYPGDAASIAALHAYWARLWNYLYRVA, 225-H: (SEQ ID NO: 30)PRRPKYPGDAASCAALHAYWARLWNYLYRVA, 225-I: (SEQ ID NO: 31)PRRPRYPGDAASIAALHAYWARLWNYLYRXA, 225-J: (SEQ ID NO: 32)PRRPRYPGDAASIAALHAYWARLWNYLYRZA, 225-K: (SEQ ID NO: 33)PRRPCYPGDAASIAALHAYWARLWNYLYRVA, 225-L: (SEQ ID NO: 34)PRRPKCPGDAASIAALHAYWARLWNYLYRVA, 225-M: (SEQ ID NO: 35)PRRPRYPGXAASIAALHAYWARLWNYLYRVA, 225-N: (SEQ ID NO: 36)PRRPRYPGZAASIAALHAYWARLWNYLYRVA, 225-4s1: (SEQ ID NO: 37)PRRPKYPGDAASIAALHAYWARLWNYLYRVR, 291-A: (SEQ ID NO: 38)PRRPKHPGHAASIAALHAYWARLWNYLYRVR, 291-1: (SEQ ID NO: 39)PRRPRHPGPNATISQLHHYWARLWNYLYRVR, 291-H: (SEQ ID NO: 40)PRRPHHPGHAASIAALHAYWARLWNYLYRVR, 291-I: (SEQ ID NO: 41)PRRPHYPGHAASIAALHAYWARLWNYLYRVR, 291-Q3: (SEQ ID NO: 42)PRRPRCPGHAASIAALHAYWARLWNYLYRVR, MY01: (SEQ ID NO: 43)GPRRPRCPGDDASIRDLLKYWWRLRLYLLAVA, RL01: (SEQ ID NO: 44)GPRRPRCPGDDASISDLLLYWLRLDRYLWAVA, RR01: (SEQ ID NO: 45)GPRRPRCPGDDASIRDLVMYWYRLYFYLEAVA, 225-1c: (SEQ ID NO: 46)PRRPKYPGDAASIAALHAYWARLWNYLYRVS, 225-4d: (SEQ ID NO: 47)RPRRPKYPGDAASIAALHAYWARLWNYLYRVS, 291-T: (SEQ ID NO: 49)PRRPRYPGDAASIAALHAYWARLWNYLYRVS, Q: (SEQ ID NO: 50)PRRPRCPGDNASIRQLHAYWQRLYAYLAAVA, and R: (SEQ ID NO: 51)PRRPRCPGDAASIAALHAYWQRLYAYLAAVA.

The peptides may comprise a sequence that is about 80% to about 99%homologous to the amino acid sequence of SEQ ID NO: 12-51. The peptidesmay comprise a sequence that is about 80% to about 99% identical to theamino acid sequence of SEQ ID NO: 12-51. The peptides may comprise asequence that that contains the amino acid sequence of SEQ ID NO: 12-51with 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid changes (e.g., aminoacid deletions and/or additions). Any of the exemplary peptides andpeptides that are at least 80% homologous or identical to the exemplarypeptides can form heterodimers or homodimers with one another.

In certain embodiments, a heterodimerized peptide comprises a primarypeptide selected from SEQ ID NO: 22, 23, and 49. In certain embodiments,a heterodimerized peptide comprises a secondary peptide selected fromSEQ ID NO: 24-27, 50, and 51. In certain embodiments, a heterodimerizedpeptide comprises a primary peptide selected from SEQ ID NO: 22, 23, and49 and and a secondary peptide selected from SEQ ID NO: 24-27, 50, and51.

In one aspect, provided are peptides the can penetrate cells. In certainembodiments, the peptides comprise reduced number of negative charges.In certain embodiments, the number of negative charges of a peptide isreduced by 1, 2, 3, 4, 5, or 6 negative charges compared to the startingpeptide. For example, introducing neutral or non-negatively chargedamino acids, such as Ala or Ser, in place of anionic residues can helpto increase cell penetration. Other residues that would be useful forincreasing cell penetration are those that are known to decrease proteinaggregation (residues that are generally not large, do not have highcharges, and/or not too hydrophobic). In certain embodiments, thedisclosed peptides comprise at least one, two, or three neutral ornon-negatively charged amino acids at positions X₁₁, X₁₅, and/or X₁₆. Incertain embodiments, the disclosed peptides comprise at least one, two,three, or four neutral or non-negatively charged amino acids atpositions X₁₁, X₁₅, X₁₆, and/or X₁₉. In certain embodiments, the neutralor non-negatively charged amino acids are Ala or Ser. In certainembodiments, the peptides comprise Ala in place of anionic residues. Incertain embodiments, the peptides comprise Ser in place of anionicresidues. In certain embodiments, the disclosed peptides comprise atleast one, two, three, or four Ala or Ser at positions X₁₁, X₁₅, X₁₆,and/or X₁₉ of any one of the peptides disclosed herein.

In one aspect, provided herein are peptides designed to prevent orminimize dimerization prior to cell penetration. The peptides disclosedherein can comprise Cys or Sec masked with small organic thiol moietiesto prevent crosslinking. In certain embodiments, the small organic thiolmoiety is —SR^(S), wherein R^(S) is a substituted or unsubstituted C₁₋₅alkyl. In certain embodiments, the small organic thiol moiety is t-butylthiol or ethanethiol. In certain embodiments, the peptide comprises asequence selected from the group consisting of SEQ ID NO: 30, 33, and34, wherein the Cys is disulfide bonded to small organic thiol moiety.In any of the foregoing embodiments or embodiments herein comprisingCys, Sec is also contemplated in place of Cys.

In another aspect, provided herein are peptides designed to crosslink toanother peptide comprising electrophilic side chains after the peptideshave penetrated the cells. In certain embodiments, peptides disclosedherein comprise residues modified with moieties capable of crosslinkingto Cys or Sec. In certain embodiments, the peptides comprises an aminoacid comprising an acrylamide moiety. In certain embodiments, thepeptides comprise L-2,4-diaminobutyric acid (Dab) residues orL-2,3-diaminopropionic acid (Dap) residues. In certain embodiments, thepeptides comprise L-2,4-diaminobutyric acid (Dab) residues orL-2,3-diaminopropionic acid (Dap) residues, wherein the Dab and Dap aremodified with acrylic acid to form a side chain comprising acrylamide.In certain embodiments, the peptide comprises a sequence selected fromthe group consisting of SEQ ID NO: 31, 32, 35, and 36, wherein X₁₈L-2,4-diaminobutyric acid (Dab) residue conjugated to acrylamide and Zis a L-2,3-diaminopropionic acid (Dap) residue conjugated to acrylamide.Dap and Dab residues conjugated to acrylamide are further describedherein. Peptide dimers can be formed from any combination of SEQ ID NO:30, 33, and 34 with SEQ ID NO: 31, 32, 35, and 36. It is understood thatCys can be replaced with Sec in any of the embodiments described herein.In certain embodiments, the disclosed peptides comprise Cys or Sec atpositions X₆, X₇, and/or X₁₄ of any one of the peptides disclosedherein. In certain embodiments, the disclosed peptides comprise an aminoacid comprising an acrylamide moiety at positions X₁₀, X₃₁, and/or X₃₂of any one of the peptides disclosed herein. In certain embodiments, thedisclosed peptides comprise Dap or Dab at positions X₁₀, X₃₁, and/or X₃₂of any one of the peptides disclosed herein, wherein the Dap or Dab aremodified with acrylic acid to form a side chain comprising acrylamide.In certain embodiments, provided is a first peptide monomer comprisingCys or Sec at positions X₆, X₇, or X₁₄ of the first peptide monomer,wherein the Cys or Sec are masked with a small organic thiol moiety asprovided herein; and a second peptide monomer comprising Dap or Dab atpositions X₁₀, X₃₁, or X₃₂ of the second peptide, wherein the Dap or Dabare modified with acrylic acid to form a side chain comprisingacrylamide.

In yet another aspect, provided herein are selective dimerdestabilization strategies to improve endosomal escape and cytosolicaccess of the dimer. Strategies provided herein include pH-induceddestabilization or bulky residue destabilization. In certainembodiments, the peptides described herein comprise one or more Hisplaced in amino acid positions such that they are spatially close to oneor more cationic residues or one or more His on the opposing monomerpeptide. In certain embodiments, the peptides comprise His placed atpositions X₆, X₇, and/or X₁₀. His placed at one, two, or three of thesepositions is applicable to any of the peptides described herein. Incertain embodiments, the peptide comprises a sequence selected from thegroup consisting of SEQ ID NO: 38 to 41.

In certain embodiments, dimer destabilization is achieved using residuescomprising bulky moieties near the dimer interface to preventdimerization. Such bulky moieties are removed after cell penetration andthe corresponding residue is free to dimerize. Examples of bulkymoieties useful for masking Cys or Sec include organic thiol molecules.In certain embodiments, the peptides described herein comprise Cys orSec protected by reaction with organic thiol molecules. In certainembodiments, the organic thiol molecules are selected from aryl thiols,heteroaryl thiols, and aliphatic thiols. In certain embodiments, theorganic thiol molecules are heteroaryl thiols. In certain embodiments,the peptides described herein comprise Cys or Sec protected by reactionwith 2,2′-Dipyridyldisulfide, 4,4′-Dipyridyldisulfide, or2,2′-Dithiobis(5-nitropyridine). In certain embodiments, the peptidescomprise a sequence selected from SEQ ID NO: 30, 33, 34, and 42, whereinthe Cys is protected by any of the foregoing organic thiol molecules. Itis understood that Cys can be replaced with Sec in any of theembodiments described herein.

In certain embodiments, any of the peptides described herein compriseCys or Sec at X₇ and Ala or Ser at one or more of X₁₁, X₁₅, X₁₆, and/orX₁₉. In certain embodiments, any of the peptides described hereincomprise Tyr at X₇ and Ala or Ser at one or more of X₁₁, X₁₅, X₁₆,and/or X₁₉.

In certain embodiments, any of the peptides described herein compriseHis at X₆ and Cys or Sec at X₇. In certain embodiments, any of thepeptides described herein comprise Cys or Sec at X₇ and His at X₁₀.

It is understood that the peptides described herein can comprise anacetylated N-terminus and/or an amidated C-terminus.

In still another aspect, provided herein is a method of treating adisease or condition associated with Ras, Myc/Max, RalA, Beta catenin,YAP/TEAD, or NEMO/IκB kinase in a subject in need thereof comprisingadministering a peptide as described herein to the subject. In certainembodiments, the disease or condition is associated with Ras. Alsoprovided herein is a method of treating a proliferative disease in asubject in need thereof comprising administering a peptide as describedherein to the subject. Exemplary diseases or conditions include variouscancers and rasopathies.

The peptides described herein are also useful in methods and systems forscreening libraries of peptides. In one aspect, provided herein aremethods and systems of screening a library of peptide dimers comprisingthe steps of transforming display cells with a vector encoding a firstpeptide and a second peptide, wherein the first and second peptidesassociate to form a peptide dimer fused to a cell wall protein,contacting the display cells with a first label, wherein the first labelcomprises a target protein and associates with a cell expressing thepeptide dimer having enhanced binding to the target and does notassociate with a cell which does not express the peptide dimer havingenhanced binding to the target; isolating the display cells with whichthe first label is associated; and identifying the first and secondpeptides which exhibit enhanced binding to the target. Alternatively,the method can comprises transforming display cells with a first vectorencoding a first peptide and second vector encoding a second peptide.

In a further aspect, provided herein are kits comprising the peptidesand dimers described herein. Also provided are nucleic acids encodingthe peptides and dimers described herein. In addition, host cellscomprising the nucleic acids, peptides, and dimers are alsocontemplated.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings are not intended to be drawn to scale. In theDrawings, for purposes of clarity, not every component may be labeled inevery drawing.

FIG. 1 shows a crystal structure of Ras bound to an effector.HRas.GppNHp is shown on the right, with nucleotide indicated in sticks;the Ras binding domain (RBD) of RalGDS is shown on the left. PDB: 1LFD.

FIG. 2 shows a yeast display system. A DNA library encoding the peptidelibrary is transformed into yeast strain EBY100, which expresses theAga2p-peptide fusion and secretes it to the cell surface. Yeast cellsare then incubated with fluorescently labeled target protein (in thiscase, Ras) and fluorescently labeled antibody to one of the epitope tags(to measure the abundance of displayed fusion protein), then screenedusing fluorescent activated cell sorting (FACS). FIG. 2 adapted fromChao, G., et al. Isolating and engineering human antibodies using yeastsurface display. Nat Protoc 1, 755-68 (2006).

FIGS. 3A-B show that aPP-M has higher thermal stability than wild-typeaPP. FIG. 3A shows CD spectra of aPP and aPP-M. FIG. 3B shows thethermal melting profile at 222 nm.

FIGS. 4A-B show library scaffolds and residues selected forrandomization. A structure of aPP are found in FIG. 4A, with randomizedresidues indicated with an arrow. FIG. 4B shows the amino acid sequences(SEQ ID NOS: 52, 7 and 54, respectively, in order of appearance) of thelibraries. An underlined X designates any amino acid.

FIG. 5 shows the PCR strategy for preparing library fragments. A set ofprimers with sufficient overlap are annealed and extended, serving astemplates for one another. Mutations are introduced through the use ofmultiple degenerate codons within each primer (site saturationmutagenesis), providing high combinatorial diversity in the resultinglibrary.

FIG. 6 shows site-specific labeling of proteins with Sfpphosphopantetheinyl transferase. The sulfhydryl moiety of CoA is reactedwith a maleimide-functionalized label of choice (e.g., biotin), then theresulting conjugate is transferred to the yBBr tag on the target proteinby Sfp.

FIGS. 7A-C show the purification of Ras proteins. FIG. 7A shows gelfiltration trace of His6-tagged (SEQ ID NO: 55) KRas G12V followingelution from cobalt resin. FIG. 7B shows reverse-phase HPLC analysis ofRas-bound nucleotides for GDP- and GTP-loaded proteins. GDP and GTPstandards elute at 12 and 15 minutes, respectively. FIG. 7C shows theMALDI-MS spectrum of Ras before and after enzymatic biotinylation bySfp.

FIG. 8 shows a SDS-PAGE gel of Ras protein samples from the purificationsteps (Coomassie stain).

FIG. 9 shows flow cytometric analysis of initial hit from aPP-scaffoldedlibrary. Yeast cells were incubated in the presence of no Ras, 500 nMKRas, 500 nM KRas and 4μM B-Raf RBD, or 500 nM KRas with 10% v/v humanserum. The 500 nM KRas sample is overlaid in the Raf and serum plots forcomparison.

FIG. 10 shows the directed evolution of aPP-scaffolded peptides. Thehits of each round were diversified by error-prone PCR, then theresulting yeast libraries were selected by magnetic-activated cellsorting (MACS) and fluorescence-activated cell sorting (FACS) for theability to bind KRas under increasingly stringent conditions (lower[KRas] and increased blocking agents). Mutations are underlined in thefirst round in which they appear; in subsequent rounds, they areindicated in italics. FIG. 10 discloses SEQ ID NOS 54, 56-68, 65, 4, 61and 72-74, respectively, in order of appearance.

FIG. 11 shows the peptides used for in vitro studies. For consistency,residue numbers are reported using the positions in the wild-type aPPpeptide. Alanine point mutations are underlined. FIG. 11 discloses SEQID NOS 8, 75, 11 and 77-85, respectively, in order of appearance.

FIGS. 12A-C show the purification of 225 peptides. Following cobaltaffinity chromatography and overnight TEV cleavage of the expressedfusion construct, the reaction was purified by reverse-phase HPLC (FIG.12A). The indicated peak, containing the 225 peptide, was collected andanalyzed by LC/MS (FIG. 12B and FIG. 12C). The different column size forthe HPLC and LC/MS instruments accounts for the discrepancy in retentiontimes between A and B. Data is shown for the 225-1 peptide

(GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYAVA (SEQ ID NO: 8)).

FIGS. 13A-B show the circular dichroism spectra of aPP-M and 225peptides. FIG. 13A shows the UV CD spectra; FIG. 13B shows the meltingprofile at 222 nm. aPP-M and 225-1 were measured at pH 8.0; 225-3 wasmeasured at pH 12 and pH 4.5 due to low solubility in the pH 5-10 range.

FIG. 14 shows fluorescence polarization measurements of the Ras-peptideinteraction. FITC-labeled 225-3 peptide was mixed with increasingconcentrations of Ras or Ras family proteins, then the fluorescencepolarization was read and plotted. Error bars are standard error of themean (SEM).

FIGS. 15A-B show surface plasmon resonance measurements of theRas-peptide interaction. Biotinylated KRas (bound to either GppNHp, FIG.15A, or GDP, FIG. 15B) was immobilized on a streptavidin capture chip,then free 225-1 peptide was injected at increasing concentrations. Thehigh affinity of the interactions permitted “single cycle” runs thatlack a regeneration step between injections and produce step-likebinding curves. Data were fit using a two-step binding model.

FIG. 16 shows positions selected for alanine mutagenesis. Residues forthe 225 peptides were modeled onto the crystal structure of aPP (PDB:1PPT). Positions chosen for mutation to alanine are indicated witharrows. Crystal structure is from Blundell, T. L., et al. X-ray analysis(1. 4-A resolution) of avian pancreatic polypeptide: Small globularprotein hormone. Proc Natl Acad Sci USA 78, 4175-9 (1981).

FIGS. 17A-C show properties of single alanine mutants of the 225-3peptide. FIG. 17A shows fluorescence polarization experiments as wereperformed above with the indicated 225-3 alanine mutant peptides andKRas(G12V)GppNHp. FIG. 17B shows CD spectra of mutants at 25° C., FIG.17C shows the melting profile at 222 nm. All CD experiments were carriedout at pH 12. Error bars are SEM.

FIGS. 18A-B show the 225-3 peptide binds endogenous Ras in cancer celllysates and blocks its interaction with Raf. Capan-1 adenocarcinomacells were lysed and incubated with 225-3 peptides and/or GST-tagged RafRBD, then either the peptide (FIG. 18A) or Raf (FIG. 18B) was pulleddown with the indicated beads. The bound samples were boiled with SDS,run on an SDS-PAGE gel, transferred to a nitrocellulose membrane, andwestern blotted with a pan-Ras antibody.

FIG. 19 shows the 225 peptides interfere with nucleotide dissociationfrom Ras. Peptides were mixed with KRas (G12V) loaded with mant-GppNHp,then GppNHp was added to 625 μM and the dissociation of mant-labelednucleotide was tracked as a decrease in fluorescence (excitation: 370nm, emission: 450 nm). Dissociation constants were calculated by fittingthe data to a one phase exponential decay with RF_(∞)=0.37.

FIGS. 20A-C show ¹H-¹⁵N HSQC (TROSY) NMR spectra of Ras in the presenceand absence of 225-1. FIG. 20A shows the TROSY of ¹⁵N-labeled KRas (WT)GDP; FIG. 20B shows the TROSY of ¹⁵N-labeled KRas with unlabeled 225-1,and FIG. 20C shows the overlay of spectra.

FIG. 21 shows that the 225 peptide binding site overlaps with the Raseffector domain. The residues in the effector domain were defined byco-crystal structures of HRas with effectors, and the peptide bindingsite was defined by the TROSY experiment with 225-1 in FIG. 20B.Residues are indicated with a black outline on the crystal structure ofKRas(WT).GppNHp (PDB: 3GFT).

FIGS. 22A-C show ¹H-¹⁵N HSQC (TROSY) NMR spectra of 225-1 in thepresence and absence of Ras. FIG. 22A shows the TROSY of ¹⁵N-labeled225-1; FIG. 22B shows the TROSY of ¹⁵N-labeled 225-1 with unlabeled KRas(G12V) GDP, and FIG. 22C shows the overlay of spectra.

FIGS. 23A-C show the head-to-tail dimerization of aPP peptides. Crystalstructure of aPP (PDB: 1PPT) shown in cartoon representation (FIG. 23A),with sticks (FIG. 23B), and with the Y7 pair shown (FIG. 23C).

FIG. 24 shows the N26A mutant can bind Ras as a heterodimer with 225-1.Yeast displaying either 225-1 or 225-1 N26A were pre-incubated with 25μM of (free) 225-1 or 225-1 N26A peptide, then pelleted and incubatedwith 500 nM KRas.

FIG. 25 shows the design of scanning mutagenesis library based on 225-1.The library was prepared by overlap extension as for the original naïvelibraries, using individual primers for each sublibrary. X was encodedby an NNK codon. FIG. 25 discloses SEQ ID NOS 65 and 86-90,respectively, in order of appearance.

FIGS. 26A-B show the 225-1 S13C/I14E mutant forms a heterodimer with225-1 that binds Ras with increased affinity. FIG. 26A shows yeastdisplaying either 225-1 or 225-1 S13C/I14E were pre-incubated with 10 uMof (free) 225-1, 225-1 alk (alkylated 225-1), or 225-1 N26A, thenpelleted and incubated with 5 nM KRas before FACS. FIG. 26B shows thealkylation of the cysteine sidechain by iodoacetamide.

FIG. 27 shows the model illustrating the location of S13 and theN-terminal cysteine. The left peptide represents 225-1 with an unreactedcysteine handle on the N-terminus, and the right peptide represents thepartner with S13 (which is cysteine in the S13C/I14E double mutant)indicated.

FIG. 28 shows the 225-1 A30R mutant is more selective for KRas (GTP)than 225-1. Yeast displaying either 225-1 or 225-1 A30R were incubatedwith 500 nM of biotinylated KRas(GTP) and 500 nM of Alexa647-labeledKRas(GDP), then washed and incubated with streptavidin-phycoerythrin(SA-PE) before sorting.

FIG. 29 shows the design of a library to identify monomeric 225derivatives. The a-helices from the 225 peptides are shown above thecorresponding helices in the new library; X₄₋₆ is the randomized loop,with X being NNK. Underlined A's replace hydrophobic amino acids thatpreviously packed with the PPII helix. FIG. 29 discloses SEQ ID NOS91-93, respectively, in order of appearance.

FIG. 30 shows binding affinity by fluorescence polarization, a standardassay for measuring dissociation constants. RDA1: K_(d)=17 nM; RDA2:K_(d)=8 nM; RDA3: K_(d)=6 nM.

FIGS. 31A-B shows a HPLC assay that can distinguish between oxidized(disulfide-crosslinked) peptide dimers from reduced (non-crosslinked)peptide monomers. By adding 5 mM or 50 mM DTT, a reducing agent muchstronger than the cellular environment, we can show that theselenocysteine-containing peptide dimers (FIG. 31B) cannot be reduced,unlike their cysteine-containing analogs (FIG. 31A). Method: peptideswere dissolved in buffer and incubated with 0 mM, 5 mM, or 50 mM DTTbefore analyzing by reverse-phase HPLC. Reduced peptides elute earlierthan oxidized peptides, as determined by LC/MS analysis of the samples.

FIG. 32 shows structures of Ras RDA1 (SEQ ID NO: 4). The first shows theoverall structure, at 2.2 Angstrom resolution. The second two showclose-ups of the primary helix with the key binding residues identified.

FIGS. 33A-B show surface plasmon resonance measurements of Ras-peptideinteractions. Biotinylated KRas (bound to either GppNHp or GDP) wasimmobilized on a streptavidin capture chip, then free dimeric peptideswere injected at increasing concentrations. The high affinity of theinteractions permitted “single cycle” runs that lack a regeneration stepbetween injections and produce step-like binding curves. Data were fitusing a two-step binding model. FIG. 33A shows SPR measurements using aheterodimer peptide comprising SEQ ID NO: 23 and 26. FIG. 33B shows SPRmeasurements using a homodimer peptide comprising SEQ ID NO: 4.

FIGS. 34A-B show live-cell microscopy with labeled peptides, performedin H358 lung adenocarcinoma cells at 5 uM peptide concentration in DMEMmedia supplemented with 10% fetal calf serum. FIG. 34A shows cellstreated with a peptide homodimer comprising SEQ ID NO: 10. FIG. 34Bshows cells treated with the 4-residue mutant peptide homodimercomprising SEQ ID NO: 28. Both peptides were labeled with fluorescein.The 4-residue mutant peptide comprising SEQ ID NO: 28 entered cellsbetter than the peptide comprising SEQ ID NO: 10. The aggregates in FIG.34A were not present in FIG. 34B, which is a consequence of increasedsolubility imparted by the mutations found in SEQ ID NO: 28 compared toSEQ ID NO: 10.

FIGS. 35A-B shows a mass chromatogram from an LC-MS analysis of peptideof SEQ ID NO: 30 mixed with a peptide of SEQ ID NO: 31, either with 1 mM(FIG. 35A) or 10 mM (FIG. 35B) glutathione.

FIGS. 36A-B shows live-cell confocal microscopy using labeled peptidedimers, performed in H358 lung adenocarcinoma cells, at 5 μMconcentration of fluorescein-labeled peptide, in DMEM media supplementedwith 10% fetal calf serum. FIG. 36A shows peptides of SEQ ID NO: 37,which lacks histidines. FIG. 36B shows peptides of SEQ ID NO: 38, whichcontains two histidines per monomer (four histidines per dimer; “Histetrad”).

FIG. 37 shows a 291-Q3 peptide of SEQ ID NO: 42 in which the Cys wasreacted with 2,2′-Dipyridyldisulfide to create a disulfide-protectedcysteine. This cysteine is uncaged in the presence of low glutathionelevels to form the disulfide-bonded species, which is a better Rasbinder. The data demonstrate an increase in Ras binding upon addition of5 mM reduced glutathione, which results in the formation of the covalentdisulfide-bonded dimer, as verified by mass spectrometry.

FIGS. 38A-C show yeast surface display binding data for peptides of SEQID NO: 43 to 45 with the corresponding protein target. FIG. 38A showsRL01 peptide of SEQ ID NO: 44 binding data to KRas and to RalA. FIG. 38Bshows RR01 peptide of SEQ ID NO: 45 binding data to KRas and to RalA.FIG. 38C shows MY01 peptide of SEQ ID NO: 43 binding data to Myc/Max.

DEFINITIONS

A “peptide” comprises a polymer of amino acid residues linked togetherby peptide (amide) bonds. The term peptide is used herein to generallyrefer to both the peptide monomer and the peptide dimer. The terms, asused herein, refers to proteins, miniproteins, polypeptides, andpeptides of any size, structure, or function. The terms may also referto dimers or oligomers of peptides. The terms, as used herein, mayinclude stapled, unstapled, stitched, and unstitched polypeptides.Typically, a peptide will be at least three amino acids long. A peptidemay refer to an individual peptide or a collection of peptides.Inventive peptides preferably can comprises only natural amino acids oralso non—natural amino acids (i.e., compounds that do not occur innature but that can be incorporated into a peptide chain) and/or aminoacid analogs as are known in the art may alternatively be employed. Oneor more of the amino acids in a peptide may be modified, for example, bythe addition of a chemical entity such as a carbohydrate group, ahydroxyl group, a phosphate group, a farnesyl group, an isofarnesylgroup, palmitoyl, geranylgeranyl, lauryl, a fatty acid group, a linkerfor conjugation, functionalization, or other modification. A peptide maybe just a fragment of a naturally occurring protein or peptide. Apeptide or polypeptide may be naturally occurring, recombinant, orsynthetic, or any combination thereof

The term “amino acid” refers to a molecule containing both an aminogroup and a carboxyl group. In certain embodiments, the amino acid is analpha-amino acid. In certain embodiments, the amino acid is a naturalamino acid. In certain embodiments, the amino acid is an non-amino acid.There are many known non-natural amino acids any of which may beincluded in the peptides of the present invention. See for example, S.Hunt, The Non-Protein Amino Acids: In Chemistry and Biochemistry of theAmino Acids, edited by G. C. Barrett, Chapman and Hall, 1985.

Exemplary amino acids include, without limitation, natural alpha-aminoacids such as D- and L-isomers of the 20 common naturally occurringalpha amino acids found in peptides, natural amino acids which are notthe 20 common naturally occurring amino acids, and unnatural alpha-aminoacids. Amino acids used in the construction of peptides of the presentinvention may be prepared by organic synthesis, or obtained by otherroutes, such as, for example, degradation of or isolation from a naturalsource. Amino acids may be commercially available or may be synthesized.Amino acids with hydrophobic side chains include Gly, Pro, Ala, Ile,Leu, Val, Phe, Met, Trp, and Tyr. In certain embodiments, amino acidswith hydrophobic side chains include Ala, Ile, Leu, and Val. Amino acidswith polar neutral side chains include Asn, Cys, Gln, Met, Ser, and Thr.Amino acids with aromatic side chains include Phe, Trp, Tyr, and His.Amino acids with hydrophobic aromatic side chains include Phe, Typ, andTyr. Amino acids with charged side chains include Asp, Glu, Arg, His,and Lys. Negatively charged side chains include Asp and Glu. Positivelycharged side chains include Arg, His, and Lys. Non-negatively chargedamino acids are selected from the group consisting of Ala, Ser, Val,Leu, Ile, Pro, Phe, Trp, Met, Gly, Thr, Cys, Tyr, Asn, and Gln.

As used herein, “amino acids capable of cross-linking the peptide withanother peptide” include amino acids that cross-link covalently andnon-covalently. For example, residues capable of covalent cross-linkinginclude, but are not limited to, Cys, Sec, amino acids comprising aacrylamide moiety such as Dap and Dab modified with acrylic acid to forma side chain with an acrylamide. Such Dab- and Dap-conjugated acrylamideresidues can crosslink to Cys or Sec residues. Amino acid residuescapable of non-covalently cross-linking the peptides include, but arenot limited to, His, Phe, Trp, Tyr.

Amino acids can be cross-linked through a disulfide bond, diseleniumbond, sulfide-selenium bond, carbon-carbon bond, amide bond, ester bond,hydrogen bond, salt bridge, pi stacking interaction, or non-polarhydrophobic interaction. In certain embodiments, two peptides areassociated through a disulfide bond. In certain embodiments, twopeptides are associated through a diselenium bond. In certainembodiments, two peptides are associated through a hydrogen bond, saltbridge, or non-polar hydrophobic interaction. In certain embodiments,two peptides are associated through pi stacking interaction. Forexample, a tyrosine on one peptide interacts with another tyrosine onanother peptide through pi stacking.

The term “homologous”, as used herein is an art-understood term thatrefers to nucleic acids or proteins that are highly related at the levelof nucleotide or amino acid sequence. Nucleic acids or proteins that arehomologous to each other are termed homologues. Homologous may refer tothe degree of sequence similarity between two sequences (i.e.,nucleotide sequence or amino acid). The homology percentage figuresreferred to herein reflect the maximal homology possible between twosequences, i.e., the percent homology when the two sequences are soaligned as to have the greatest number of matched (homologous)positions. Homology can be readily calculated by known methods such asthose described in: Computational Molecular Biology, Lesk, A. M., ed.,Oxford University Press, New York, 1988; Biocomputing: Informatics andGenome Projects, Smith, D. W., ed., Academic Press, New York, 1993;Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press,1987; Computer Analysis of Sequence Data, Part I, Griffin, A. M., andGriffin, H. G., eds., Humana Press, New Jersey, 1994; and SequenceAnalysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press,New York, 1991; each of which is incorporated herein by reference.Methods commonly employed to determine homology between sequencesinclude, but are not limited to those disclosed in Carillo, H., andLipman, D., SIAM J Applied Math., 48:1073 (1988); incorporated herein byreference. Techniques for determining homology are codified in publiclyavailable computer programs. Exemplary computer software to determinehomology between two sequences include, but are not limited to, GCGprogram package, Devereux, J., et al., Nucleic Acids Research, 12(1),387 (1984)), BLASTP, BLASTN, and PASTA Atschul, S. F. et al., J Molec.Biol., 215, 403 (1990)).

The term “homologous”, as used herein is an art-understood term thatrefers to nucleic acids or polypeptides that are highly related at thelevel of nucleotide or amino acid sequence. Nucleic acids orpolypeptides that are homologous to each other are termed “homologues.”

The term “homologous” refers to a comparison between two sequences. Twonucleotide sequences are considered to be homologous if the polypeptidesthey encode are at least about 50-60% identical, preferably about 70%identical, for at least one stretch of at least 20 amino acids.Preferably, homologous nucleotide sequences are also characterized bythe ability to encode a stretch of at least 4-5 uniquely specified aminoacids. Both the identity and the approximate spacing of these aminoacids relative to one another must be considered for nucleotidesequences to be considered homologous. For nucleotide sequences lessthan 60 nucleotides in length, homology is determined by the ability toencode a stretch of at least 4-5 uniquely specified amino acids.

As used herein, the term “identity” refers to the overall relatednessbetween polymeric molecules, e.g., between nucleic acid molecules (e.g.DNA molecules and/or RNA molecules) and/or between polypeptidemolecules. Calculation of the percent identity of two nucleic acidsequences, for example, can be performed by aligning the two sequencesfor optimal comparison purposes (e.g., gaps can be introduced in one orboth of a first and a second nucleic acid sequences for optimalalignment and non-identical sequences can be disregarded for comparisonpurposes). In certain embodiments, the length of a sequence aligned forcomparison purposes is at least 30%, at least 40%, at least 50%, atleast 60%, at least 70%, at least 80%, at least 90%, at least 95%, or100% of the length of the reference sequence. The nucleotides atcorresponding nucleotide positions are then compared. When a position inthe first sequence is occupied by the same nucleotide as thecorresponding position in the second sequence, then the molecules areidentical at that position. The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences, taking into account the number of gaps, and the length ofeach gap, which needs to be introduced for optimal alignment of the twosequences. The comparison of sequences and determination of percentidentity between two sequences can be accomplished using a mathematicalalgorithm. For example, the percent identity between two nucleotidesequences can be determined using methods such as those described inComputational Molecular Biology, Lesk, A. M., ed., Oxford UniversityPress, New York, 1988; Biocomputing: Informatics and Genome Projects,Smith, D. W., ed., Academic Press, New York, 1993; Sequence Analysis inMolecular Biology, von Heinje, G., Academic Press, 1987; ComputerAnalysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G.,eds., Humana Press, New Jersey, 1994; and Sequence Analysis Primer,Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991;each of which is incorporated herein by reference. For example, thepercent identity between two nucleotide sequences can be determinedusing the algorithm of Meyers and Miller (CABIOS, 1989, 4:11-17), whichhas been incorporated into the ALIGN program (version 2.0) using aPAM120 weight residue table, a gap length penalty of 12 and a gappenalty of 4. The percent identity between two nucleotide sequences can,alternatively, be determined using the GAP program in the GCG softwarepackage using an NWSgapdna.CMP matrix. Methods commonly employed todetermine percent identity between sequences include, but are notlimited to those disclosed in Carillo, H., and Lipman, D., SIAM JApplied Math., 48:1073 (1988); incorporated herein by reference.Techniques for determining identity are codified in publicly availablecomputer programs. Exemplary computer software to determine homologybetween two sequences include, but are not limited to, GCG programpackage, Devereux, J., et al., Nucleic Acids Research, 12(1), 387(1984)), BLASTP, BLASTN, and FASTA Atschul, S. F. et al., J. Molec.Biol., 215, 403 (1990)).

As used herein, “cross-linking” peptides refers to either covalentlycross-linking peptides or non-covalently cross-linking peptides. Incertain embodiments, the peptides are covalently associated. Covalentinteraction is when two peptides are covalently connected through alinker group such as a natural or non-natural amino acid side chain. Inother embodiments, the peptides are non—covalently associated.Non—covalent interactions include hydrogen bonding, van der Waalsinteractions, hydrophobic interactions, magnetic interactions, andelectrostatic interactions. The peptides herein comprise an amino acidcapable of cross-linking the peptide with another peptide (e.g.,cysteine, selenocysteine, amino acids comprising a acrylamide moiety,Dap-conjugated acrylamide, Dab-conjugated acrylamide). In the case ofpeptide dimers, the peptide dimers comprise amino acids cross-linkingthe first peptide with the second peptide. The peptides may alsocomprise natural or non-natural amino acids capable of cross-linking thepeptide with another peptide. The peptide dimers may comprise natural ornon-natural amino acids cross-linking the first peptide with the secondpeptide.

“Peptide stapling” is one method for crosslinking within a peptide(intrapeptide) or between different peptides (interpeptide). Peptidestapling describes a synthetic methodology wherein two olefin-containingsidechains present in a peptide or different peptides are covalentlyjoined (“stapled”) using a ring—closing metathesis (RCM) reaction toform a crosslink (see, the cover art for J. Org. Chem. (2001) vol. 66,issue 16 describing metathesis-based crosslinking of alpha-helicalpeptides; Blackwell et al.; Angew Chem. Int. Ed. (1994) 37:3281; and US7,192,713). “Peptide stitching” involves multiple “stapling” events in asingle polypeptide chain to provide a multiply stapled (also known as“stitched”) polypeptide (see, for example, Walensky et al., Science(2004) 305:1466-1470; U.S. Pat. Nos. 7,192,713; 7,786,072; 8,592,377;7,192,713; U.S. Patent Application Publication No. 2006/0008848; U.S.Patent Application Publication No. 2012/0270800; InternationalPublication No. WO 2008/121767 and International Publication No. WO2011/008260). Stapling of a peptide using all-hydrocarbon crosslinks hasbeen shown to help maintain its native conformation and/or secondarystructure, particularly under physiologically relevant disorders (seeSchafmiester et al., J. Am. Chem. Soc. (2000) 122:5891-5892; Walensky etal., Science (2004) 305:1466-1470). In certain embodiments, thenon-natural amino acids found in the peptides described herein comprisea side chain capable of being covalently joined using olefin moieties(i.e., “stapled together”) using a cross-linking reaction such as aring—closing metathesis (RCM) reaction. Additional description of therelated peptide stapling or peptide stitching can be found inWO2010/011313, WO2012/040459, WO2012/174423, and PCT/U52013/062004, U.S.Ser. No. 61/478845, 61/478862, 61/705950, 61/789157, and 61/708371, allof which are incorporated by reference herein.

The term “Ras” refers to the Ras protein family or mutants thereof. Rasproteins are small cytosolic GTPases that function in several signaltransduction pathways, and that can activate a number of downstreamproteins (effectors) by binding through the Ras effector domain. Rasproteins are switched by upstream factors between the guanosinetriphosphate (GTP, “on”) and guanosine diphosphate (GDP, “off”) states.There are three Ras isoforms in humans: KRas, HRas, and NRas, with twosplice variants of KRas, KRas4A and KRas4B. Active Ras proteins arelocalized to membranes by the post-translational attachment of lipids(typically farnesyl or geranylgeranyl groups), and typically activateeffector proteins by binding their Ras binding domains (RBDs) andthereby recruiting them to the membrane, where they are activatedthrough a variety of mechanisms.

As used herein, the terms “disease” and “disorder” are usedinterchangeably.

A “subject” to which administration is contemplated includes, but is notlimited to, humans (i.e., a male or female of any age group, e.g., apediatric subject (e.g, infant, child, adolescent) or adult subject(e.g., young adult, middle—aged adult or senior adult)) and/or othernon-human animals, for example mammals (e.g., primates (e.g., cynomolgusmonkeys, rhesus monkeys); commercially relevant mammals such as cattle,pigs, horses, sheep, goats, cats, and/or dogs), birds (e.g.,commercially relevant birds such as chickens, ducks, geese, and/orturkeys), reptiles, amphibians, and fish. In certain embodiments, thenon-human animal is a mammal. The non-human animal may be a male orfemale and at any stage of development. A non-human animal may be atransgenic animal.

As used herein, and unless otherwise specified, the terms “treat,”“treating” and “treatment” contemplate an action that occurs while asubject is suffering from a disorder which reduces the severity of thedisorder or retards or slows the progression of the disorder(“therapeutic treatment”), and also contemplates an action that occursbefore a subject begins to suffer from the disorder and which inhibitsor reduces the severity of the disorder (“prophylactic treatment”).

In general, the “effective amount” of a peptide refers to an amountsufficient to elicit the desired biological response, i.e., treating thedisorder. As will be appreciated by those of ordinary skill in this art,the effective amount of a peptide of the invention may vary depending onsuch factors as the desired biological endpoint, the pharmacokinetics ofthe compound, the disorder being treated, the mode of administration,and the age, health, and the subject. An effective amount encompassestherapeutic and prophylactic treatment.

As used herein, and unless otherwise specified, a “therapeuticallyeffective amount” of a peptide is an amount sufficient to provide atherapeutic benefit in the treatment of the disorder or to delay orminimize one or more symptoms associated with the disorder. Atherapeutically effective amount of a peptide means an amount oftherapeutic agent, alone or in combination with other therapies, whichprovides a therapeutic benefit in the treatment of the disorder. Theterm “therapeutically effective amount” can encompass an amount thatimproves overall therapy, reduces or avoids symptoms or causes of thedisorder, or enhances the therapeutic efficacy of another therapeuticagent.

As used herein, and unless otherwise specified, a “prophylacticallyeffective amount” of a peptide is an amount sufficient to prevent thedisorder, or one or more symptoms associated with the disorder orprevent its recurrence. A prophylactically effective amount of a peptidemeans an amount of a therapeutic agent, alone or in combination withother agents, which provides a prophylactic benefit in the prevention ofthe disorder. The term “prophylactically effective amount” can encompassan amount that improves overall prophylaxis or enhances the prophylacticefficacy of another prophylactic agent.

The term “RASopathy” or “RASopathies” are a clinically defined group ofmedical genetic syndromes caused by germline mutations in genes thatencode components or regulators of the Ras/mitogen-activated proteinkinase (MAPK) pathway. These disorders include neurofibromatosis type 1,Noonan syndrome, Noonan syndrome with multiple lentigines, capillarymalformation-arteriovenous malformation syndrome, Costello syndrome,cardio-facio-cutaneous (CFC) syndrome, and Legius syndrome. Because ofthe common underlying Ras/MAPK pathway dysregulation, the RASopathiesexhibit numerous overlapping phenotypic features. The Ras/MAPK pathwayplays an essential role in regulating the cell cycle and cellulargrowth, differentiation, and senescence, all of which are critical tonormal development. Therefore, Ras/MAPK pathway dysregulation hasprofound deleterious effects on both embryonic and later stages ofdevelopment. The Ras/MAPK pathway has been studied in cancer and is atarget for small-molecule inhibition to treat various malignancies.

The term “aliphatic” refers to alkyl, alkenyl, alkynyl, and carbocyclicgroups. Likewise, the term “heteroaliphatic” refers to heteroalkyl,heteroalkenyl, heteroalkynyl, and heterocyclic groups.

The term “alkyl” refers to a radical of a straight—chain or branchedsaturated hydrocarbon group having from 1 to 10 carbon atoms (“C₁₋₁₀alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms(“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbonatoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl grouphas 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkylgroup has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, analkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments,an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In someembodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In someembodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”).Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), propyl(C₃) (e.g., n—propyl, isopropyl), butyl (C₄) (e.g., n—butyl, tert—butyl,sec-butyl, iso-butyl), pentyl (C₅) (e.g., n-pentyl, 3-pentanyl, amyl,neopentyl, 3-methyl-2-butanyl, tertiary amyl), and hexyl (C₆) (e.g.,n-hexyl). Additional examples of alkyl groups include n-heptyl (C₇),n-octyl (C₈), and the like. Unless otherwise specified, each instance ofan alkyl group is independently unsubstituted (an “unsubstituted alkyl”)or substituted (a “substituted alkyl”) with one or more substituents(e.g., halogen, such as F). In certain embodiments, the alkyl group isan unsubstituted C₁₋₁₀ alkyl (such as unsubstituted C₁₋₆ alkyl, e.g.,—CH₃ (Me), unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g.,unsubstituted n-propyl (n-Pr), unsubstituted isopropyl (i-Pr)),unsubstituted butyl (Bu, e.g., unsubstituted n-butyl (n-Bu),unsubstituted tent-butyl (tent-Bu or t-Bu), unsubstituted sec-butyl(sec-Bu), unsubstituted isobutyl (i-Bu)). In certain embodiments, thealkyl group is a substituted C₁₋₁₀ alkyl (such as substituted C₁₋₆alkyl, e.g., —CF₃, Bn).

The term “aryl” refers to a radical of a monocyclic or polycyclic (e.g.,bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or14 π electrons shared in a cyclic array) having 6-14 ring carbon atomsand zero heteroatoms provided in the aromatic ring system (“C₆₋₁₄aryl”). In some embodiments, an aryl group has 6 ring carbon atoms (“C₆aryl”; e.g., phenyl). In some embodiments, an aryl group has 10 ringcarbon atoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and2-naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms(“C₁₄ aryl”; e.g., anthracyl). “Aryl” also includes ring systems whereinthe aryl ring, as defined above, is fused with one or more carbocyclylor heterocyclyl groups wherein the radical or point of attachment is onthe aryl ring, and in such instances, the number of carbon atomscontinue to designate the number of carbon atoms in the aryl ringsystem. Unless otherwise specified, each instance of an aryl group isindependently unsubstituted (an “unsubstituted aryl”) or substituted (a“substituted aryl”) with one or more substituents. In certainembodiments, the aryl group is an unsubstituted C₆₋₁₄ aryl. In certainembodiments, the aryl group is a substituted C₆₋₁₄ aryl.

The term “heteroaryl” refers to a radical of a 5-14 membered monocyclicor polycyclic (e.g., bicyclic, tricyclic) 4n+2 aromatic ring system(e.g., having 6,10, or 14 π electrons shared in a cyclic array) havingring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ringsystem, wherein each heteroatom is independently selected from nitrogen,oxygen, and sulfur (“5-14 membered heteroaryl”). In heteroaryl groupsthat contain one or more nitrogen atoms, the point of attachment can bea carbon or nitrogen atom, as valency permits. Heteroaryl polycyclicring systems can include one or more heteroatoms in one or both rings.“Heteroaryl” includes ring systems wherein the heteroaryl ring, asdefined above, is fused with one or more carbocyclyl or heterocyclylgroups wherein the point of attachment is on the heteroaryl ring, and insuch instances, the number of ring members continue to designate thenumber of ring members in the heteroaryl ring system. “Heteroaryl” alsoincludes ring systems wherein the heteroaryl ring, as defined above, isfused with one or more aryl groups wherein the point of attachment iseither on the aryl or heteroaryl ring, and in such instances, the numberof ring members designates the number of ring members in the fusedpolycyclic (aryl/heteroaryl) ring system. Polycyclic heteroaryl groupswherein one ring does not contain a heteroatom (e.g., indolyl,quinolinyl, carbazolyl, and the like) the point of attachment can be oneither ring, i.e., either the ring bearing a heteroatom (e.g.,2—indolyl) or the ring that does not contain a heteroatom (e.g.,5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-8 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-6 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In someembodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unlessotherwise specified, each instance of a heteroaryl group isindependently unsubstituted (an “unsubstituted heteroaryl”) orsubstituted (a “substituted heteroaryl”) with one or more substituents.In certain embodiments, the heteroaryl group is an unsubstituted 5-14membered heteroaryl. In certain embodiments, the heteroaryl group is asubstituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing 1 heteroatom include,without limitation, pyrrolyl, furanyl, and thiophenyl. Exemplary5-membered heteroaryl groups containing 2 heteroatoms include, withoutlimitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, andisothiazolyl. Exemplary 5-membered heteroaryl groups containing 3heteroatoms include, without limitation, triazolyl, oxadiazolyl, andthiadiazolyl. Exemplary 5-membered heteroaryl groups containing 4heteroatoms include, without limitation, tetrazolyl. Exemplary6-membered heteroaryl groups containing 1 heteroatom include, withoutlimitation, pyridinyl. Exemplary 6-membered heteroaryl groups containing2 heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, andpyrazinyl. Exemplary 6-membered heteroaryl groups containing 3 or 4heteroatoms include, without limitation, triazinyl and tetrazinyl,respectively. Exemplary 7-membered heteroaryl groups containing 1heteroatom include, without limitation, azepinyl, oxepinyl, andthiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, withoutlimitation, indolyl, isoindolyl, indazolyl, benzotriazolyl,benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl,benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl,benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, andpurinyl. Exemplary 6,6-bicyclic heteroaryl groups include, withoutlimitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl,cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplarytricyclic heteroaryl groups include, without limitation,phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl,phenoxazinyl and phenazinyl.

The term “thiol” refers to the group —SH (e.g., found in Cys sidechain), —SR^(S), or a molecule comprising a —S-S— moiety. For example,an “organic thiol molecule” includes molecules such as2,2′-Dipyridyldisulfide, 4,4′-Dipyridyldisulfide, or2,2′-Dithiobis(5-nitropyridine). The phrase “small organic thiolmoieties” include organic groups comprising a sulfur, such as —SR^(S),wherein R^(S) is a substituted or unsubstituted C₁₋₅ alkyl. Suchmoieties are able to bond to other thiol or selenium moieties throughdisulfide bonding or selenium-sulfide bonding, respectively. Forexample, a Cys side chain bonded to t-butyl thiol has the followingstructure:

Provided below are a list of abbreviations that are used herein.

Dab L-2,4-diaminobutyric acid

Dap L-2,3-diaminopropionic acid

PPI Protein-protein interaction

RBD Ras binding domain

GAP GTPase activating protein

GRP Guanine nucleotide releasing proteins

bHLHZip Basic helix-loop-helix leucine zipper

PCR Polymerase chain reaction

FACS Fluorescence-activated cell sorting

NMR Nuclear magnetic resonance

aPP Avian pancreatic polypeptide

PPII Polyproline type II

Tm Melting transition

CD Circular dichroism

PI3K Phosphatidylinositide 3-kinase

MACS Magnetic-activated cell sorting

NA-PE Neutravidin-phycoerythrin

SA-PE Streptavidin-allophycocyanin

IMAC Immobilized metal affinity chromatography

CoA Coenzyme A

GTP Guanosine triphosphate

GDP Guanosine diphosphate

GppNHp Guanosine 5′-[β,γ-imido]triphosphate

GppCp β,γ-methyleneguanosine 5′-triphosphate

IPTG Isopropyl β-D-1-thiogalactopyranoside

LB Lysogeny Broth

MALDI-MS Matrix-assisted laser desorption/ionization mass spectrometry

HPLC High-performance liquid chromatography

TEV Tobacco etch protease

LC/MS Liquid chromatography-mass spectrometry

DMSO Dimethyl sulfoxide

TCEP Tris(2-carboxyethyl)phosphine

Kd Dissociation constant

FP Fluorescence polarization

FITC Fluorescein isothiocyanate

SPR Surface plasmon resonance

RU Resonance units

SDS-PAGE Sodium dodecyl sulfate-polyacrylamide gel electrophoresis

GST Glutathione-S-transferase

mantGppNHp N-methylanthraniloyl ester of GppNHp

HSQC Heteronuclear quantum spin correlation spectroscopy

NLS Nuclear localization signals

MBP Maltose binding protein

SEC selenocysteine

Detailed Description of Certain Embodiments of the Invention

While advances have been made in understanding the molecular mechanismsof human disease, our ability to exploit these discoveries fortherapeutic benefit is frequently limited by the inability to make drugsthat target the processes which are responsible for the disease. Manydiseases can be linked to the aberrant activity of proteins, and whilethe development of inhibitors of enzymes and extracellular targets isoften feasible, these proteins account for only a small fraction of allproteins. The remaining proteins are, in most cases, consideredtherapeutically intractable and are sometimes referred to as“undruggable.” An example of an “undruggable” protein target is Ras,which is linked to both the initiation and progression of a wide arrayof human diseases, such as cancers, yet remains out of the reach ofcontemporary therapeutics. This is primarily a consequence of theintracellular localization of Ras, which renders this proteininaccessible to biologics, and their intractability to small molecules,which are typically capable of entering cells. Attempts to target theone hydrophobic pocket (the nucleotide binding site) of Ras has not beensuccessful, largely due to the extremely high (picomolar) affinity ofthe Ras proteins for guanine nucleotides, and the relatively highabundance of these nucleotides in cells. Many peptide therapeutics arelimited by their ability to enter cells. However, certain small proteins(peptides) are capable of entering cells with the appropriate chemicalmodifications. Peptides are often large enough to engage proteinsurfaces, and if modified to possess high affinity and specificity fortheir protein targets, they have been shown to act as effectiveinhibitors of protein-protein interactions in vivo.

Provided herein are peptides that inhibit protein-protein interactionsof protein targets that cannot currently be treated by conventionaltherapy. The peptides are based on a scaffold that includes analpha-helical domain. The alpha-helix is the most common secondarystructure in proteins, and alpha-helices are often involved in criticalprotein-protein interactions. Alpha-helices are therefore attractive aspotential therapeutics, in particular because they might be used todisrupt protein-protein interactions responsible for disease.

In certain embodiments, the peptides provided herein comprise apolyproline type-II helix domain, a linker domain, and an alpha-helicaldomain. These proteins may bind protein targets and thereby disruptprotein-protein interactions. Examples of targets of the inventiveproteins include the Ras oncoprotein. The peptides bind the surfaces oftheir targets and block key interactions with partner molecules that arerequired for the target's activity (e.g., the oncogenic activity ofRas). Other targets include the Myc/Max heterodimer and RalA protein.

The peptides provided herein are based on the pancreatic polypeptidefamily. In certain embodiments, the peptides provided herein are basedon avian, human, bovine, ovine, porcine, canine pancreatic polypeptides,and mutants thereof. In certain embodiments, the peptides providedherein are based on avian pancreatic polypeptide (aPP), and derivativesand mutants thereof. The peptides provided herein comprise a polyprolinetype-II helix domain, a linker domain, and a C-terminal alpha-helicaldomain, and the peptides include a moiety capable of cross-linking thepeptide with another peptide. An example of a general peptide dimer isshown in FIGS. 23A-C. Also provided herein are peptide dimers of twopeptides, each comprising a polyproline type-II helix domain, a linkerdomain, and a C-terminal alpha-helix domain, wherein each peptideincludes a moiety capable of covalently or non-covalently cross-linkingwith another peptide monomer. The peptide dimers can be homodimers orheterodimers.

The term “peptide” is used herein to refer to both the peptide monomerand peptide dimer. In certain embodiments, the peptides are chemicallystabilized and/or cell-permeable. Examples of chemical stabilizationincludes crosslinking as described herein, peptide stapling, peptidestitching, or peptide cyclization (e.g., the N-terminus and C-terminusare connected with an amide bond to form a continuous amide backbone, ora sidechain on the N-terminus crosslinks to a sidechain on theC-terminus). Resistance to proteolysis can be accomplished using variousmethods including but not limited to D-amino acid incorporation,end-capping, or cyclization of the individual peptide monomers. Incertain embodiments, cyclization is by head-to-tail cyclization. Thisexploits the fact that the N- and C-termini are spatially close, as seenin our crystal structure. This could be accomplished by coupling the N-and C-termini to form an amide bond, or by coupling the sidechains oftwo residues that are the N- and C-termini or are close to them. Stapledor stitched peptides have been described in, for example, Walensky etal., Science (2004) 305:1466-1470; U.S. Pat. Nos. 8,592,377; 7,192,713;U.S. Patent Application Publication No. 2006/0008848; U.S. PatentApplication Publication No. 2012/0270800; International Publication No.WO 2008/121767 and International Publication No. WO 2011/008260, each ofwhich are incorporated herein by reference.

Further provided herein are methods of screening a library of peptidedimers using a display technology (e.g., yeast cell display, bacterialcell display, or phage display) for enhanced binding to a protein targetsuch as Ras, Myc/Max, RalA, or another target. Also provided herein arepharmaceutical compositions, methods, uses, and kits comprising peptidesuseful as inhibitors of protein-protein interactions. In some cases, thepharmaceutical compositions, methods, uses, and kits comprising peptidesare useful as inhibitors of protein-protein interactions that cannotcurrently be targeted by conventional therapy such as the Rasoncoprotein and its intereactions with effector molecules. Exemplarydiseases that may be prevented and/or treated with peptides describedherein include proliferative diseases (e.g., cancers) and otherdiseases, disorders, or conditions (e.g., rasopathies).

Peptides

The peptides are based on the aPP scaffold,GPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVA (SEQ ID NO: 49), and bind a proteintarget. In certain embodiments, the peptides bind Ras, Myc/Max, and/orRalA. In certain embodiments, the peptides bind Ras. In certainembodiments, the peptides bind Myc/Max. In certain embodiments, thepeptides bind RalA. In certain embodiments, the peptides bind both KRasand RalA.

In certain embodiments, provided herein are peptides comprising thesequence:X₁PX₃X₄PX₆X₇PGX₁₀X₁₁AX₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA (SEQ IDNO: 1), wherein the peptides comprise one to two amino acids capable ofcross-linking the peptide with another peptide. In certain embodiments,the amino acids capable of cross-linking the peptide with anotherpeptide is capable of covalent cross-linking. Also provided are peptidedimers comprising a first peptide associated with a second peptide,wherein the first and second peptides each independently comprise apeptide of SEQ ID NO: 1, and wherein the first and second peptides eachcomprises one to two amino acids cross-linking the first peptide withthe second peptide. In certain embodiments, the peptide dimer iscovalently cross-linked. X₁ is Gly, Arg, or an amino acid capable ofcross-linking the peptide with another peptide. In certain embodiments,X₁ is absent from SEQ ID NO: 1. X₃, X₄, and X₆ are each independently acharged amino acid. X₁₀ is a charged amino acid. X₁₁ is a charged aminoacid or an amino acid capable of cross-linking the peptide with anotherpeptide. X₇ is Tyr or an amino acid capable of cross-linking the peptidewith another peptide. X₁₃ is Ser or an amino acid capable ofcross-linking the peptide with another peptide. X₁₄ is Ile or Glu. X₁₅is Glu, Asp, Gln, or Gly. X₁₈ is an aromatic or hydrophobic amino acid.X₁₉ is Glu, Asp, Gln, Ala, or Trp. X₂₁, X₂₅, and X₂₉ are eachindependently a Tyr, Phe, Trp, His, or an amino acid with a cyclohexylside chain, wherein the Tyr, Phe, Trp, or cylohexyl side chain can besubstituted with one or more fluorines. X₂₂ is Ala, Gly, Ser, or Val.X₂₆ is Asn, Leu, Ile, or His. X₃₀ is Ala or Arg.

In certain embodiments, provided herein are peptides comprising thesequence: X₁PX₃X₄PX₆X₇P GX₁₀X1AX₁₃X₁₄X₁₅DLX₁₈X₁₉X₂₀X₂₁X₂₂X₂₃LX₂₅X₂₆YLX₂₉X₃₀VA (SEQ ID NO: 12),wherein the peptides comprise one to two amino acids capable ofcross-linking the peptide with another peptide. In certain embodiments,the amino acids capable of cross-linking the peptide with anotherpeptide is capable of covalent cross-linking. Also provided are peptidedimers comprising a first peptide associated with a second peptide,wherein the first and second peptides each independently comprise apeptide of SEQ ID NO: 12, wherein the first and second peptides eachcomprises one to two amino acids cross-linking the first peptide withthe second peptide. In certain embodiments, the peptide dimer iscovalently cross-linked. X₁ is Gly, Arg, or an amino acid capable ofcross-linking the peptide with another peptide. In certain embodiments,X₁ is absent from SEQ ID NO: 12. X₃, X₄, and X₆ are each independently acharged amino acid. X₁₀ is a charged amino acid. X₁₁ is a charged aminoacid or an amino acid capable of cross-linking the peptide with anotherpeptide. X₇ is Tyr or an amino acid capable of cross-linking the peptidewith another peptide. X₁₃ is Ser, Pro, or an amino acid capable ofcross-linking the peptide with another peptide. X₁₄ is Ile, Glu, or Val.X₁₈ is Glu, Asp, Gln, or Gly. X₁₈ is an aromatic or hydrophobic aminoacid. X₁₉ is Glu, Asp, Gln, Ala, Trp, or Arg. X₂₀ is Tyr or Phe. X₂₁is aTyr, Phe, Trp, His, or an amino acid with a cyclohexyl side chain,wherein Tyr, Phe, Trp, cylohexyl side chain can be substituted with oneor more fluorines. X₂₂ is Ala, Gly, Ser, Val, or Asn. X₂₃ is Arg or Asp.X₂₅ is a Tyr, Phe, Trp, His, Gln, or an amino acid with a cyclohexylside chain, wherein Tyr, Phe, Trp, cylohexyl side chain can besubstituted with one or more fluorines. X₂₆ is Asn, Leu, Ile, His, orGln. X₂₉ is a Tyr, Phe, Trp, His, Asn, or an amino acid with acyclohexyl side chain, wherein Tyr, Phe, Trp, cylohexyl side chain canbe substituted with one or more fluorines. X₃₀ is Ala, Arg, or Val.

In certain embodiments, provided herein are peptides comprising thesequence:X-₆X-₅X-₄X-₃X-₂X-₁X₁PX₃X₄PX₆X₇PGX₁₀X₁₁AX₁₃X₁₄X₁₅X₁₆LX₁₈X₁₉X₂₀X₂₁X₂₂X₂₃LX₂₅X₂₆YLX₂₉X₃₀X₃₁X₃₂ (SEQ ID NO: 13), wherein the peptides comprise one to twoamino acids capable of cross-linking the peptide with another peptide.In certain embodiments, the amino acids capable of cross-linking thepeptide with another peptide is capable of covalent cross-linking. Alsoprovided are peptide dimers comprising a first peptide associated with asecond peptide, wherein the first and second peptides each independentlycomprise a peptide of SEQ ID NO: 13, wherein the first and secondpeptides each comprises one to two amino acids cross-linking the firstpeptide with the second peptide. In certain embodiments, the peptidedimer is covalently cross-linked. X₃ and X₄ are each independently aneutral or charged amino acid. X₆ is a charged amino acid or an aminoacid capable of cross-linking the peptide with another peptide. X₇ isTyr, His, or an amino acid capable of cross-linking the peptide withanother peptide. X₁₀ is Pro, charged amino acid, or an amino acidcapable of cross-linking the peptide with another peptide. X₁₁ is Ala,Ser, neutral or charged amino acid, or an amino acid capable ofcross-linking the peptide with another peptide. X₁₃ is Ser, Pro, Thr, oran amino acid capable of cross-linking the peptide with another peptide.X₁₄ is Ile, Glu, Val, Leu, or an amino acid capable of cross-linking thepeptide with another peptide. X₁₅ is Glu, Lys, Arg, Ala, Ser, Asp, Gln,or Gly. X₁₆ is Asp, Glu, Gln, Ala, or Ser. X₁₈ is an aromatic orhydrophobic amino acid. X₁₉ is Glu, Lys, Leu, Met, His, Asp, Gln, Ala,Ser, Trp, or Arg. X₂₀is Tyr or Phe. X₂₁ is Gln, Tyr, Phe, Trp, His, oran amino acid with a cyclohexyl side chain, wherein Tyr, Phe, Trp,cylohexyl side chain can be substituted with one or more fluorines. X₂₂is Ala, Gln, Trp, Leu, Tyr, Gly, Ser, Val, or Asn. X₂₃ is Arg, Asp, Leu,or Ala. X₂₅ is Gln, Tyr, Phe, Trp, His, Asp, or an amino acid with acyclohexyl side chain, wherein Tyr, Phe, Trp, cylohexyl side chain canbe substituted with one or more fluorines. X₂₆ is Asn, Ala, Leu, Arg,Phe, Ile, His, or Gln. X₂₉ is Ala, Leu, Glu, Asn, Gln, Tyr, Phe, Trp,His, or an amino acid with a cyclohexyl side chain, wherein Tyr, Phe,Trp, cylohexyl side chain can be substituted with one or more fluorines.X₃₀ is Ala, Arg or Val. X₃₁ is V or an amino acid capable ofcross-linking the peptide with another peptide. X₃₂ is V, Ala, Arg, Ser,or an amino acid capable of cross-linking the peptide with anotherpeptide.

Optional residues of SEQ ID NO: 13 are X-₆, X-₅, X-₄, X-₃, X-₂, X-₁, andX₁. If X-₆ is present, then X-₆ is Gly and X-₅ to X₁ are present. If X-₅is present, then X-₅ is Cys or Sec and X-₄ to X₁ are present. If X-₄ ispresent, then X-₄ is Gly and X-₃ to X₁ are present. If X-₃ is present,then X-₃ is Gly and X-₂ to X₁ are present. If X-₂ is present, then X-₂is Pro, Cys, Sec, or Gly and X-₁ and X₁ are present. If X-₁ is present,then X-₁ is Arg or Gly and X₁ is present. When X₁ is present, X₁ is Gly,Arg, or an amino acid capable of cross-linking the peptide with anotherpeptide. Additional embodiments for X₁ are described herein.

In certain embodiments of SEQ ID NO: 13, X-₆ to X₁ are not present, X₁₁,X₁₅, X₁₆, X₁₉ are each Ala or Ser, X₁₈ , is His, X₂₀is Tyr, and X₂₆ isAsn. In certain embodiments of SEQ ID NO: 13, X-₆ to X₁ are not present,X₁₁, X₁₅, X₁₆, X₁₉ are each Ala, X₁₈ is His, X₂₀is Tyr, and X₂₆ is Asn.

In certain embodiments, provided herein are peptides comprising thesequence: X₁PX₃X₄PX₆X₇PGX₁₀AAX₁₃X₁₄AALHAYX₂₁AX₂₃LX₂₅NYLX₂₉X₃₀VX₃₂ (SEQID NO: 48), wherein the peptides comprise one to two amino acids capableof cross-linking the peptide with another peptide. In certainembodiments, the amino acids capable of cross-linking the peptide withanother peptide is capable of covalent cross-linking. X₁ is optionallypresent. When present, X₁ is Gly, Arg, or an amino acid capable ofcross-linking the peptide with another peptide. X₃, X₄, and X₆ are eachindependently a neutral or positively charged amino acid. X₇ is Tyr oran amino acid capable of cross-linking the peptide with another peptide.X₁₀ is Asp or a neutral amino acid. X₁₃ is Ser, Thr or an amino acidcapable of cross-linking the peptide with another peptide. X₁₄ is Ile orLeu. X₂₁, X₂₅, X₂₉ are each independently a Tyr, Phe, Trp, His, or anamino acid with a cyclohexyl side chain, wherein Tyr, Phe, Trp,cylohexyl side chain can be substituted with one or more fluorines. X₂₃is Arg, Leu or Ala. X₃₀ is Ala or Arg. X₃₂ is Ala, Ser, or Arg.

In certain embodiments, provided are peptides comprising the sequence ofSEQ ID NO: 48 except one or more Ala at positions 11, 15, 16, and 19 arereplaced with Ser.

In certain embodiments, the peptide dimer is a homodimer. In certainembodiments, the peptide dimer is a heterodimer. In certain embodiments,the peptide dimer is a dimer though covalent cross-linking. For example,Cys, Sec, Dap modified with acrylic acid or Dab modified with acrylicacid are used as covalent cross-linkers. Other amino acids comprising anacrylamide, vinyl sulfonamide, iodoacetamide moieties, or other knownMichael acceptors would be useful for cross-linking. In certainembodiments, the peptide dimer is a dimer though non-covalentcross-linking. For example, His, Tyr, Phe, or Trp are used asnon-covalent cross-linkers.

In certain embodiments, the peptides do not comprise a sequence of SEQID NO: 7. In certain embodiments, the peptide monomer cannothomodimerize with the same peptide monomer but can heterodimerize with adifferent peptide monomer. This can be accomplished, for example, withthe use of a “bump-hole” system whereby a residue in one peptide cannotbe accommodated in a dimer with the same peptide (e.g., due to steric orotherwise unfavorable interaction), but can be accommodated in a dimerwith a second peptide. The same would be true for the second peptide; inthis way, neither peptide can form a homodimer but are able toheterodimerize.

Exemplary peptide monomers include, but are not limited to:

RDA1: (SEQ ID NO: 4) GPRRPRCPGDDASIEDLHEYWARLWNYLYAVA, RDA2:(SEQ ID NO: 5) GPRRPRCPGDDASIEDLHEYWARLWNYLYRVA, RDA3: (SEQ ID NO: 6)GRRPRRPRCPGDDASIEDLHEYWARLWNYLYAVA, aPP-M: (SEQ ID NO: 7)GPRRPRVPGDDAPVEDLIRFYNDLQQYLNVVA, 225-1: (SEQ ID NO: 8)GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYAVA, 225-1 S13C/I14E: (SEQ ID NO: 9)GCGGPRRPRYPGDDACEEDLHEYWARLWNYLYAVA, 225-1 A30R: (SEQ ID NO: 10)GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYRVA, 225-3: (SEQ ID NO: 11)GCGGPRRPRRPRYPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 14)PRRPRCPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 15)PRRPRCPGDDASIEDLHEYWARLWNYLYRVA, (SEQ ID NO: 16)RRPRRPRCPGDDASIEDLHEYWARLWNYLYAVA, (SEQ ID NO: 17)PRRPRYPGDDAPVEDLIRFYNDLQQYLNVVA, (SEQ ID NO: 18)PRRPRYPGDDASIEDLHEYWARLWNYLYAVA (SEQ ID NO: 19)CGGPRRPRYPGDDACEEDLHEYWARLWNYLYAVA (SEQ ID NO: 20)PRRPRYPGDDASIEDLHEYWARLWNYLYRVA (SEQ ID NO: 21)PRRPRRPRYPGDDASIEDLHEYWARLWNYLYAVA (SEQ ID NO: 22)PRRPRCPGDDASLEDLHEYWARLWNYLYRVA, (SEQ ID NO: 23)PRRPRCPGDQASLEELHEYWARLWNYLYRVA, (SEQ ID NO: 24)PRRPRCPGDNASIKQLHAYWNRLYAYLAAVA, (SEQ ID NO: 25)PRRPRCPGDDASIEDLHEYWQRLYAYLAAVA, (SEQ ID NO: 26)PRRPRCPGDNASIKQLHAYWQRLYAYLAAVA, (SEQ ID NO: 27)PRRPRCPGDNASIRQLHAYWQRLYAYLAAVA, (SEQ ID NO: 28)GCGGPRRPRYPGDAASIAALHAYWARLWNYLYRVA, (SEQ ID NO: 29)PRRPRYPGDAASIAALHAYWARLWNYLYRVA, 225-H: (SEQ ID NO: 30)PRRPKYPGDAASCAALHAYWARLWNYLYRVA, 225-I: (SEQ ID NO: 31)PRRPRYPGDAASIAALHAYWARLWNYLYRXA, 225-J: (SEQ ID NO: 32)PRRPRYPGDAASIAALHAYWARLWNYLYRZA, 225-K: (SEQ ID NO: 33)PRRPCYPGDAASIAALHAYWARLWNYLYRVA, 225-L: (SEQ ID NO: 34)PRRPKCPGDAASIAALHAYWARLWNYLYRVA, 225-M: (SEQ ID NO: 35)PRRPRYPGXAASIAALHAYWARLWNYLYRVA, 225-N: (SEQ ID NO: 36)PRRPRYPGZAASIAALHAYWARLWNYLYRVA, 225-4s1: (SEQ ID NO: 37)PRRPKYPGDAASIAALHAYWARLWNYLYRVR, 291-A: (SEQ ID NO: 38)PRRPKHPGHAASIAALHAYWARLWNYLYRVR, 291-1: (SEQ ID NO: 39)PRRPRHPGPNATISQLHHYWARLWNYLYRVR, 291-H: (SEQ ID NO: 40)PRRPHHPGHAASIAALHAYWARLWNYLYRVR, 291-I: (SEQ ID NO: 41)PRRPHYPGHAASIAALHAYWARLWNYLYRVR, 291-Q3: (SEQ ID NO: 42)PRRPRCPGHAASIAALHAYWARLWNYLYRVR, MY01: (SEQ ID NO: 43)GPRRPRCPGDDASIRDLLKYWWRLRLYLLAVA, RL01: (SEQ ID NO: 44)GPRRPRCPGDDASISDLLLYWLRLDRYLWAVA, RR01: (SEQ ID NO: 45)GPRRPRCPGDDASIRDLVMYWYRLYFYLEAVA, 225-1c: (SEQ ID NO: 46)PRRPKYPGDAASIAALHAYWARLWNYLYRVS, 225-4d: (SEQ ID NO: 47)RPRRPKYPGDAASIAALHAYWARLWNYLYRVS, 291-T: (SEQ ID NO: 49)PRRPRYPGDAASIAALHAYWARLWNYLYRVS, Q: (SEQ ID NO: 50)PRRPRCPGDNASIRQLHAYWQRLYAYLAAVA, and R: (SEQ ID NO: 51)PRRPRCPGDAASIAALHAYWQRLYAYLAAVA.

In certain embodiments, the peptides comprises an inter-monomercross-linking amino acid for the purpose of stabilizing the dimer. Theinter-monomer cross-linking amino acid can be at any position of SEQ IDNO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 1 of SEQID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 6 of SEQID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 7 of SEQID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 10 ofSEQ ID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 11 ofSEQ ID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 13 ofSEQ ID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 31 ofSEQ ID NO: 1 or 96, 12, 13 or 48. In certain embodiments, the peptidescomprises an inter-monomer cross-linking amino acid at position 32 ofSEQ ID NO: 1 or 96, 12, 13 or 48.

In certain embodiments, a cross-linking amino acid at a specificposition of SEQ ID NO: 1 or 96, 12, 13 or 48 in a first peptide wouldcrosslink to a cross-linking amino acid at the same position of a secondpeptide. In certain embodiments, a cross-linking amino acid at aspecific position of SEQ ID NO: 1 or 96, 12, 13 or 48 in a first peptidewould crosslink to a cross-linking amino acid at a different position ofa second peptide. In certain embodiments, a cross-linking amino acid atposition 7 of SEQ ID NO: 1 or 96, 12, 13 or 48 in a first peptide wouldcrosslink to a cross-linking amino acid at position 7 of a secondpeptide. In certain embodiments, a cross-linking amino acid at position1 of SEQ ID NO: 1 or 96, 12, 13 or 48 in a first peptide would crosslinkto a cross-linking amino acid at positions 11 or 13 of a second peptide.

In certain embodiments, the peptides comprises an inter-monomercross-linking amino acid at position -2 of SEQ ID NO: 1 or 96, 12, 13,or 48. In certain embodiments, a cross-linking amino acid at position -2of SEQ ID NO: 1 or 96, 12, 13 or 48 in a first peptide would crosslinkto a cross-linking amino acid at positions 11 or 13 of a second peptide.

In certain embodiments, inter-monomer cross-linking amino acid is acysteine. In certain embodiments, inter-monomer cross-linking amino acidis a selenocysteine. In certain embodiments, inter-monomer cross-linkingamino acid is an amino acid capable of forming a disulfide bond. Incertain embodiments, inter-monomer cross-linking amino acid is an aminoacid capable of forming a diselenide bond. In certain embodiments,inter-monomer cross-linking amino acid is an amino acid capable offorming a bond with a Cys or Sec. For example, electrophilic moietiessuch as those with acrylamide, vinyl sulfonamide, iodoacetamidemoieties, or other known Michael acceptors.

Peptide properties to be improved include binding affinity, stability,and cell permeability and can be accomplished, for example, by mutatingone or more amino acid residues in one or more peptide domains. Thepeptides can be made cell permeable by conjugation to a cell-penetratingpeptide (such as TAT, antennapedia, transportan, and polyarginine) or toa stapled peptide. Other methods of improving peptide properties areknown to those skilled in the art such as ligating the peptides to otherdrugs such as a drug-antibody conjugate, which are useful, for example,for tissue-specific targeting purposes or increasing potency or ligatingthe peptides to polyethylene glycol or similar molecules to improvehalf-life and slow renal clearance. In certain embodiments, thepolyproline type-II helix domain has been engineered to have improvedproperties. In certain embodiments, the loop/linker domain has beenengineered to have improved properties. In certain embodiments, theloop/linker domain is a type-I beta-turn. In certain embodiments, theC-terminal alpha-helix domain has been engineered to have improvedproperties. In certain embodiments, the charge on the peptide has beenengineered to improve cell permeability. For example, the number ofnegatively charged (Asp, Glu) residues would be decreased, the number ofpositively charged (Arg, Lys, His) residues would be increased, and/orthe number of hydrophobic (Tyr, Trp, Phe, Leu, Ile, Met) residues. Asfurther disclosed herein, in certain embodiments, certain residues ofthe peptides are mutated to Ala and/or Ser. For example, at least one,two, three, or four residues selected from X₁₁, X₁₅, X₁₆, and X₁₉ can bemutated to Ala and/or Ser. In certain embodiments, negatively chargedresidues are mutated to Ala and/or Ser. In certain embodiments, at leastone, two, three, or four negatively charged residues residues atpositions X₁₁, X₁₅, X₁₆, and X₁₉ are mutated to Ala and/or Ser. Incertain embodiments, the peptide's ability to bind serum proteins hasbeen engineered to improve pharmacokinetics. In certain embodiments, thepeptide is delivered using nanoparticles.

In certain embodiments, the peptide's ability to bind a second targethas been engineered to recruit the second target to Ras. A peptide orpeptide library would have residues mutated or randomized on the PPIIhelix, the loop, and/or the the part of the alpha helix not involved inbinding to the first target. Mutated or randomized residues can be usedfor both the first or the second monomer of a heterodimer. In certainembodiments, the loop/linker domain is a type-I beta-turn. In certainembodiments, the peptides used herein are useful for selective tissuetargeting. Examples of a second target include serum proteins such asserum albumin and serum retinoid binding protein, recycling receptorsthat are targets for ADC conjugation such as CD-20, transferrin receptorand insulin receptor for tissue targeting, the liver GalNAc receptor forliver delivery, and the Neonatal Fc receptor.

The first peptide and the second peptide can be associated covalently.The first peptide and the second peptide can also be associatednon-covalently. Any covalent bond or non-covalent interaction may beused to form the dimer. In certain embodiments, the first peptide andthe second peptide are associated through a disulfide bond, diselenidebond, carbon-carbon bond, amide bond, ester bond, hydrogen bond, saltbridge, pi stacking interaction, or non-polar hydrophobic interaction.In certain embodiments, the first peptide and the second peptide isassociated through a disulfide bond. In certain embodiments, the firstpeptide and the second peptide is associated through a diselenide bond.In certain embodiments, the first peptide and the second peptide isassociated through a carbon-carbon bond, amide bond, ester bond,hydrogen bond, salt bridge, pi stacking interaction, or non-polarhydrophobic interaction.

The peptides can each comprise one amino acid capable of cross-linkingthe peptide with another peptide. The peptides can each comprise twoamino acids capable of cross-linking the peptide with another peptide.The peptide dimers can comprise a first and a second peptide, eachcomprising one amino acid cross-linking the first peptide with thesecond peptide. The peptide dimers can comprise a first and a secondpeptide, each comprising two amino acids cross-linking the first peptidewith the second peptide. In certain embodiments the cross-links arecovalent. In certain embodiments the cross-links are non-covalent.

In certain embodiments, X₁ is an amino acid capable of cross-linking thefirst peptide with the second peptide. In certain embodiments, X₁ is anamino acid cross-linking a first peptide with a second peptide. Incertain embodiments, X₁ is a natural or non-natural amino acid capableof cross-linking the peptide with another peptide. In certainembodiments, X₁ is a natural or non-natural amino acid cross-linking thefirst peptide with the second peptide. In certain embodiments, X₁ isCys, Sec, Phe, Trp, or Tyr. In certain embodiments, X₁ is Cys, Sec. Incertain embodiments, X₁ is Cys. In certain embodiments, X₁ is Sec. Incertain embodiments, X₁ is Phe, Trp, or Tyr.

In certain embodiments, each of X₃, X₄, and X₆ is independently acharged amino acid. In certain embodiments, each of X₃, X₄, and X₆ isindependently a basic amino acid with a charged side chain. In certainembodiments, each of X₃, X₄, and X₆ is independently a positivelycharged amino acid. In certain embodiments, each of X₃, X₄, and X₆ isindependently Arg, Lys, or His. In certain embodiments, each of X₃, X₄,and X₆ is independently Arg. In certain embodiments, each of X₃, X₄, andX₆ is independently Lys. In certain embodiments, each of X₃, X₄, and X₆is independently His. In certain embodiments, each of X₃, X₄, and X₆ canbe the same or different amino acids. In certain embodiments, each ofX₃, X₄, and X₆ are the same amino acids. In certain embodiments, each ofX₃, X₄, and X₆ are the different amino acids. In certain embodiments,each of X₃, X₄, and X₆ is an amino acid that provides stability such asthrough electrostatic effects with other amino acids within the peptideor with amino acids in another peptide. In certain embodiments, X₃, X₄,and X₆ are each independently a negatively charged amino acid. Incertain embodiments, each of X₃, X₄, and X₆ is independently Asp or Glu.

In certain embodiments, X₆ is an amino acid capable of cross-linking thepeptide with another peptide. In certain embodiments, X₆ is a natural ornon-natural amino acid capable of cross-linking the peptide with anotherpeptide. In certain embodiments, X₆ is a natural or non-natural aminoacid cross-linking the first peptide with the second peptide. In certainembodiments, X₆ is Cys, Sec, Phe, Trp, or Tyr. In certain embodiments,X₆ is Cys or Sec. In certain embodiments, X₆ is Cys. In certainembodiments, X₆ is Sec. In certain embodiments, X₆ is Phe, Trp, or Tyr.

In certain embodiments, X₆ is Cys or Sec; and X₇ is Tyr.

In certain embodiments, X₇ is Tyr or an amino acid capable ofcross-linking the first peptide with the second peptide. In certainembodiments, X₇ is Tyr, His, or an amino acid capable of cross-linkingthe first peptide with the second peptide. In certain embodiments, X₇ isTyr. In certain embodiments, X₇ is His. In certain embodiments, X₇ is anamino acid cross-linking a first peptide with a second peptide. Incertain embodiments, X₇ is a natural or non-natural amino acid capableof cross-linking the peptide with another peptide. In certainembodiments, X₇ is a natural or non-natural amino acid cross-linking thefirst peptide with the second peptide. In certain embodiments, X₇ is apositively or negatively charged amino acid. In certain embodiments, X₇is Cys, Sec, Phe, Trp, or Tyr. In certain embodiments, X₇ is Cys, Sec,Tyr, or His. In certain embodiments, X₇ is Cys. In certain embodiments,X₇ is Sec. In certain embodiments, X₇ is Phe, Trp, or Tyr. In certainembodiments, X₇ is Y and X₆ is Cys or Sec.

In certain embodiments, X₁₀ is an amino acid with a charged side chain.In certain embodiments, X₁₀ is a negatively charged amino acid. Incertain embodiments, X₁₀ is Glu or Asp. In certain embodiments, X₁₀ isGlu, Asp, or Ala. In certain embodiments, X₁₀ is Glu. In certainembodiments, X₁₀ is Asp. In certain embodiments, X₁₀ is Ala. In certainembodiments, X₁₀ is a positively charged amino acid. In certainembodiments, X₁₀ is Arg, His, or Lys. In certain embodiments, X₁₀ isAsp, His, or Pro. In certain embodiments, X₁₀ is Asp, His, Pro, or anamino acid comprising an acrylamide moiety. In certain embodiments, X₁₀is Arg. In certain embodiments, X₁₀ is His. In certain embodiments, X₁₀is Lys. In certain embodiments, X₁₀ is Pro. In certain embodiments, X₁₀is an amino acid comprising an acrylamide moiety. In certainembodiments, the amino acid comprising an acrylamide moiety is Dab- andDap-conjugated acrylamide residues

In certain embodiments, X₁₀ is an amino acid capable of cross-linkingthe peptide with another peptide. In certain embodiments, X₁₀ is anatural or non-natural amino acid capable of cross-linking the peptidewith another peptide. In certain embodiments, X₁₀ is a natural ornon-natural amino acid cross-linking the first peptide with the secondpeptide. In certain embodiments, X₁₀ is Cys, Sec, Phe, Trp, or Tyr. Incertain embodiments, X₁₀ is Cys. In certain embodiments, X₁₀ is Sec. Incertain embodiments, X₁₀ is Phe, Trp, or Tyr. In certain embodiments,X₁₀ is L-2,4-diaminobutyric acid (Dab) conjugated to acrylamide orL-2,3-diaminopropionic acid (Dap) conjugated to acrylamide, as describedfurther herein.

In certain embodiments, X₁₁ is an amino acids with a charged sidechains. In certain embodiments, X₁₁ is a negatively charged amino acid.In certain embodiments, X₁₁ is Glu or Asp. In certain embodiments, X₁₁is Glu. In certain embodiments, X₁₁ is Asp. In certain embodiments, X₁₁is a positively charged amino acid. In certain embodiments, X₁₁ is Arg,His, or Lys. In certain embodiments, X₁₁ is Arg. In certain embodiments,X₁₁ is His. In certain embodiments, X₁₁ is Lys. In certain embodiments,X₁₁ is neutral amino acid. In certain embodiments, X₁₁ is an amino acidwith hydrophobic side chain. In certain embodiments, X₁₁ is Asp, Gln,Asn, Ala, or Ser. In certain embodiments, X₁₁ is Ala, Ile, Leu, Val. Incertain embodiments, X₁₁ is Ala. In certain embodiments, X₁₁ is Ser. Incertain embodiments, X₁₁ is Asp or Ala. In certain embodiments, X₁₁ isAsp or an amino acid capable of cross-linking the first peptide with thesecond peptide. In certain embodiments, X₁₁ is Asp. In certainembodiments, X₁₁ is an amino acid cross-linking a first peptide with asecond peptide. In certain embodiments, X₁₁ is a natural or non-naturalamino acid capable of cross-linking the peptide with another peptide. Incertain embodiments, X₁₁ is a natural or non-natural amino acidcross-linking the first peptide with the second peptide. In certainembodiments, X₁₁ is Cys, Sec, Phe, Trp, or Tyr. In certain embodiments,X₁₁ is Cys. In certain embodiments, X₁₁ is Sec. In certain embodiments,X₁₁ is Phe, Trp, or Tyr.

In certain embodiments, X₁₃ is Ser, Pro, or Thr. In certain embodiments,X₁₃ is Ser. In certain embodiments, X₁₃ is Pro. In certain embodiments,X₁₃ is Thr or Ala. In certain embodiments, X₁₃ is an amino acid capableof cross-linking the first peptide with the second peptide. In certainembodiments, X₁₃ is an amino acid cross-linking a first peptide with asecond peptide. In certain embodiments, X₁₃ is a natural or non-naturalamino acid capable of cross-linking the peptide with another peptide. Incertain embodiments, X₁₃ is a natural or non-natural amino acidcross-linking the first peptide with the second peptide. In certainembodiments, X₁₃ is Cys, Sec, Phe, Trp, or Tyr. In certain embodiments,X₁₃ is Cys. In certain embodiments, X₁₃ is Sec. In certain embodiments,X₁₃ is Phe, Trp, or Tyr.

In certain embodiments, X₁₄ is Ile or Glu. In certain embodiments, X₁₄is Ile. In certain embodiments, X₁₄ is Glu. In certain embodiments, X₁₄is Leu or Asp. certain embodiments, X₁₄ is Ile, Val, Glu, Leu, or anamino acid cross-linking a first peptide with a second peptide. Incertain embodiments, X₁₄ is Cys. In certain embodiments, X₁₄ is Sec.

In certain embodiments, X₁₅ is Glu, Asp, Gln, or Gly. In certainembodiments, X₁₅ is Glu, Lys, Arg, Ser, Asp, Gln, Gly, or Ala. Incertain embodiments, X₁₅ is Glu. In certain embodiments, X₁₅ is Asp. Incertain embodiments, X₁₅ is Gln. In certain embodiments, X₁₅ is Gly. Incertain embodiments, X₁₅ is Ala.

In certain embodiments, X₁₆ is Asp, Glu, Gln, Ala, or Ser. In certainembodiments, X₁₆ is Asp. In certain embodiments, X₁₆ is Glu. In certainembodiments, X₁₆ is Gln. In certain embodiments, X₁₆ is Ala. In certainembodiments, X₁₆ is Ser.

In certain embodiments, X₁₈ is an aromatic amino acid. In certainembodiments, X₁₈ is a hydrophobic amino acid. In certain embodiments,X₁₈ is His, Phe, Tyr, Trp, Ala, Val, Leu, Ile, or Met. In certainembodiments, X₁₈ is His. In certain embodiments, X₁₈ is Phe, Tyr, orTrp. In certain embodiments, X₁₈ is Ala, Val, Leu, Ile, or Met. Incertain embodiments, X₁₈ is Ala, Val, Leu, or Ile. In certainembodiments, X₁₈ is Met. In certain embodiments, X₁₈ is Ala. In certainembodiments, X₁₈ is Val. In certain embodiments, X₁₈ is Leu. In certainembodiments, X₁₈ is Ile.

In certain embodiments, X₁₉ is Glu, Asp, Gln, Ala, or Trp. In certainembodiments, X₁₉ is Glu, Asp, Gln, Ala, Ser, Trp, Arg, Lys, Leu, Met, orHis. In certain embodiments, X₁₉ is Glu, Asp, Gln, Ala, Trp, Arg, orHis. In certain embodiments, X₁₉ is Glu. In certain embodiments, X₁₉ isAsp. In certain embodiments, X₁₉ is Gln. In certain embodiments, X₁₉ isAla. In certain embodiments, X₁₉ is Ser. In certain embodiments, X₁₉ isTrp. In certain embodiments, X₁₉ is Arg. In certain embodiments, X₁₉ isLys. In certain embodiments, X₁₉ is Leu. In certain embodiments, X₁₉ isMet. In certain embodiments, X₁₉ is His.

In certain embodiments, X₂₀is Tyr or Phe. In certain embodiments, X₂₀isTyr. In certain embodiments, X₂₀is Phe.

In certain embodiments, X₂₁, X₂₅, and X₂₉ are each a hydrophobic and/orlarge amino acid. In certain embodiments, X₂₁ is Trp. In certainembodiments, X₂₁ is Tyr. In certain embodiments, X₂₁ is Phe. In certainembodiments, X₂₁ is His. In certain embodiments, X₂₁ is Gln. In certainembodiments, X₂₅ is Trp. In certain embodiments, X₂₅ is Tyr. In certainembodiments, X₂₅ is His. In certain embodiments, X₂₅ is Phe. In certainembodiments, X₂₅ is His. In certain embodiments, X₂₉ is Tyr. In certainembodiments, X₂₉ is Trp. In certain embodiments, X₂₉ is Phe. In certainembodiments, X₂₉ is His. In certain embodiments, each of X₂₁, X₂₅, X₂₉can independently be Tyr, Trp, Phe, His, or an amino acid with acyclohexyl side chain, wherein Tyr, Phe, Trp, or the cyclohexyl sidechain is optionally fluorinated. In certain embodiments, X₂₅ is Tyr,Phe, Trp, His, Gln, Arg, or Asp. In certain embodiments, X₂₉ is Tyr,Phe, Trp, His, Gln, Arg, Asp, Asn, Ala, Leu, or Glu.

In certain embodiments, X₂₂ is a small amino acid. In certainembodiments, X₂₂ is Ala. In certain embodiments, X₂₂ is Gly, Ser, orVal. In certain embodiments, X₂₂ is Gly, Ser, Val, or Asn. In certainembodiments, X₂₂ is Gly. In certain embodiments, X₂₂ is Ser. In certainembodiments, X₂₂ is Val. In certain embodiments, X₂₂ is Ala, Gly, Ser,Val, Asn, Gln, Trp, Leu, or Tyr

In certain embodiments, X₂₃ is Arg or Asp. In certain embodiments, X₂₆is Asn, Leu, Ile, or His. In certain embodiments, X₂₆ is Asn, Leu, Ile,His, Gln, Arg, Phe, or Ala. In certain embodiments, X₂₆ is Asn. Incertain embodiments, X₂₆ is Leu. In certain embodiments, X₂₆ is Ile. Incertain embodiments, X₂₆ is His.

In certain embodiments, X₃₀is Ala or Arg. In certain embodiments, X₃₀isAla, Arg, or Val. In certain embodiments, X₃₀is Arg. In certainembodiments, X₃₀is Ala. In certain embodiments, X₃₀is Val.

In certain embodiments, X₃₁ is an amino acid capable of cross-linkingthe peptide with another peptide. In certain embodiments, X₃₁ is anatural or non-natural amino acid capable of cross-linking the peptidewith another peptide. In certain embodiments, X₃₁ is a natural ornon-natural amino acid cross-linking the first peptide with the secondpeptide. In certain embodiments, X₃₁ is Val or an amino acid capable ofcross-linking the peptide with another peptide. In certain embodiments,X₃₁ is Cys, Sec, Phe, Trp, or Tyr. In certain embodiments, X₃₁ is Cys.In certain embodiments, X₃₁ is Sec. In certain embodiments, X₃₁ is Phe,Trp, or Tyr. In certain embodiments, X₃₁ is Dap-conjugated acrylamide.In certain embodiments, X₃₁ is Dab-conjugated acrylamide.

In certain embodiments, X₃₂ is Ala, Arg, Ser. In certain embodiments,X₃₂ is Ala. In certain embodiments, X₃₂ is Arg. In certain embodiments,X₃₂ is Ser. In In certain embodiments, X₃₂ is an amino acid capable ofcross-linking the peptide with another peptide. In certain embodiments,X₃₂ is a natural or non-natural amino acid capable of cross-linking thepeptide with another peptide. In certain embodiments, X₃₂ is a naturalor non-natural amino acid cross-linking the first peptide with thesecond peptide. In certain embodiments, X₃₂ is Cys, Sec, Phe, Trp, orTyr. In certain embodiments, X₃₂ is Cys. In certain embodiments, X₃₂ isSec. In certain embodiments, X₃₂ is Phe, Trp, or Tyr. In certainembodiments, X₃₂ is Arg or Ala. In certain embodiments, X₃₂ is Dab- orDap-conjugated acrylamide.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% homologous to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about84% to about 99% homologous to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about87% to about 99% homologous to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% homologous to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about93% to about 99% homologous to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 85%, 90%, 95%, 98%, or 99% homologous to the amino acidsequences provided herein.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% identical to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about84% to about 99% identical to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about87% to about 99% identical to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% identical to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is about93% to about 99% identical to the amino acid sequences provided herein.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 85%, 90%, 95%, 98%, or 99% identical to the amino acidsequences provided herein.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% homologous to the amino acid sequence of SEQ ID NO: 1or 96. In certain embodiments, the peptide comprises a sequence that isabout 85% to about 99% homologous to the amino acid sequence of SEQ IDNO: 1 or 96. In certain embodiments, the peptide comprises a sequencethat is about 90% to about 99% homologous to the amino acid sequence ofSEQ ID NO: 1 or 96. In certain embodiments, the peptide comprises asequence that is about 95% to about 99% homologous to the amino acidsequence of SEQ ID NO: 1 or 96. In certain embodiments, the peptidecomprises a sequence that is about 97% to about 99% homologous to theamino acid sequence of SEQ ID NO: 1 or 96. In certain embodiments, thepeptide comprises a sequence that is about 98% to about 99% homologousto the amino acid sequence of SEQ ID NO: 1 or 96. In certainembodiments, the peptide comprises a sequence that is at least about80%, 85%, 90%, 95%, 98%, or 99% homologous to the amino sequence of SEQID NO: 1 or 96. The foregoing values are applicable to SEQ ID NO: 12,13, and 48.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% identical to the amino acid sequence of SEQ ID NO: 1 or96. In certain embodiments, the peptide comprises a sequence that isabout 84% to about 99% identical to the amino acid sequence of SEQ IDNO: 1 or 96. In certain embodiments, the peptide comprises a sequencethat is about 87% to about 99% identical to the amino acid sequence ofSEQ ID NO: 1 or 96. In certain embodiments, the peptide comprises asequence that is about 90% to about 99% identical to the amino acidsequence of SEQ ID NO: 1 or 96. In certain embodiments, the peptidecomprises a sequence that is about 93% to about 99% identical to theamino acid sequence of SEQ ID NO: 1 or 96. In certain embodiments, thepeptide comprises a sequence that is about 96% to about 99% identical tothe amino acid sequence of SEQ ID NO: 1 or 96. In certain embodiments,the peptide comprises a sequence that is at least about 80%, 84%, 87%,90%, 93%, or 96% identical to the amino sequence of SEQ ID NO: 1 or 96.The foregoing values are applicable to SEQ ID NO: 12, 13, and 48.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 1 or 96 by 1, 2, 3, 4, 5, 6,7, 8, 9, or 10 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 1 amino acid. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 2 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 3 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 4 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 5 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 6 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 7 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 8 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 9 amino acids. In certain embodiments, the peptidecomprises a sequence that differs from the amino acid sequence of SEQ IDNO: 1 or 96 by 10 amino acids. The foregoing differences are alsoapplicable to SEQ ID NO: 12, 13, and 48.

In certain embodiments, the peptide comprises a sequence ofGPRRPRCPGDDASIEDLHEYWARLWNYLYAVA (SEQ ID NO: 4). In certain embodiments,the peptide comprises a sequence of GPRRPRCPGDDASIEDLHEYWARLWNYLYRVA(SEQ ID NO: 5). In certain embodiments, the peptide comprises a sequenceof GRRPRRPRCPGDDASIEDLHEYWARLWNYLYAVA (SEQ ID NO: 6). In certainembodiments, the peptide comprises a sequence ofGPRRPRYPGDDAPVEDLIRFYNDLQQYLNVVA (SEQ ID NO: 7). In certain embodiments,the peptide comprises a sequence of GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYAVA(SEQ ID NO: 8). In certain embodiments, the peptide comprises a sequenceof GCGGPRRPRYPGDDACEEDLHEYWARLWNYLYAVA (SEQ ID NO: 9). In certainembodiments, the peptide comprises a sequence ofGCGGPRRPRYPGDDASIEDLHEYWARLWNYLYRVA (SEQ ID NO: 10). In certainembodiments, the peptide comprises a sequence ofGCGGPRRPRRPRYPGDDASIEDLHEYWARLWNYLYAVA (SEQ ID NO: 11). In certainembodiments, the peptide comprises a sequence of SEQ ID NO: 14-51.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% homologous to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about85% to about 99% homologous to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% homologous to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about95% to about 99% homologous to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about97% to about 99% homologous to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about98% to about 99% homologous to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 85%, 90%, 95%, 98%, or 99% homologous to the aminosequence of SEQ ID NO: 4. The foregoing values are applicable to SEQ IDNO: 14-51.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% identical to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about84% to about 99% identical to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about87% to about 99% identical to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% identical to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about93% to about 99% identical to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is about96% to about 99% identical to the amino acid sequence of SEQ ID NO: 4.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 84%, 87%, 90%, 93%, or 96% identical to the aminosequence of SEQ ID NO: 4. The foregoing values are applicable to SEQ IDNO: 14-51.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 4 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 4 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 4 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 4 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 4 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 4 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 4 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 4 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 4 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 4 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 4 by 10 amino acids. The foregoingvalues are applicable to SEQ ID NO: 14-51.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% homologous to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about85% to about 99% homologous to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% homologous to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about95% to about 99% homologous to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about97% to about 99% homologous to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about98% to about 99% homologous to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 85%, 90%, 95%, 98%, or 99% homologous to the aminosequence of SEQ ID NO: 5.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% identical to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about84% to about 99% identical to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about87% to about 99% identical to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% identical to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about93% to about 99% identical to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is about96% to about 99% identical to the amino acid sequence of SEQ ID NO: 5.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 84%, 87%, 90%, 93%, or 96% identical to the aminosequence of SEQ ID NO: 5.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 5 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 5 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 5 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 5 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 5 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 5 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 5 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 5 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 5 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 5 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 5 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% homologous to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about85% to about 99% homologous to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% homologous to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about95% to about 99% homologous to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about97% to about 99% homologous to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about98% to about 99% homologous to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 85%, 90%, 95%, 98%, or 99% homologous to the aminosequence of SEQ ID NO: 6.

In certain embodiments, the peptide comprises a sequence that is about80% to about 99% identical to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about84% to about 99% identical to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about87% to about 99% identical to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about90% to about 99% identical to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about93% to about 99% identical to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is about96% to about 99% identical to the amino acid sequence of SEQ ID NO: 6.In certain embodiments, the peptide comprises a sequence that is atleast about 80%, 84%, 87%, 90%, 93%, or 96% identical to the aminosequence of SEQ ID NO: 6.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 6 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 6 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 6 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 6 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 6 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 6 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 6 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 6 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 6 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 6 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 6 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% homologous to SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 85% to about99% homologous to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 90% to about99% homologous to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 95% to about99% homologous to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 97% to about99% homologous to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 98% to about99% homologous to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is at least about80%, 85%, 90%, 95%, 98%, or 99% homologous to the amino sequence of SEQID NO: 7.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% homologous to SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 85% to about99% identical to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 90% to about99% identical to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 95% to about99% identical to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 97% to about99% identical to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is about 98% to about99% identical to the amino acid sequence of SEQ ID NO: 7. In certainembodiments, the peptide comprises a sequence that is at least about80%, 85%, 90%, 95%, 98%, or 99% identical to the amino sequence of SEQID NO: 7.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 7 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 7 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 7 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 7 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 7 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 7 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 7 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 7 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 7 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 7 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 7 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% homologous to SEQ ID NO: 8. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% homologous to SEQ ID NO: 8. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% homologous to SEQID NO: 8.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% identical to SEQ ID NO: 8. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% identical to SEQ ID NO: 8. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% identical to SEQID NO: 8.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 8 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 8 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 8 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 8 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 8 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 8 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 8 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 8 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 8 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 8 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 8 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% homologous to SEQ ID NO: 9. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% homologous to SEQ ID NO: 9. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% homologous to SEQID NO: 9.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% identical to SEQ ID NO: 9. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% identical to SEQ ID NO: 9. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% identical to SEQID NO: 9.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 9 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 9 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 9 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 9 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 9 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 9 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 9 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 9 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 9 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 9 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 9 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% homologous to SEQ ID NO: 10. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% homologous to SEQ ID NO: 10. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% homologous to SEQID NO: 10.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% identical to SEQ ID NO: 10. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% identical to SEQ ID NO: 10. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% identical to SEQID NO: 10.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 9 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 10 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 10 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 10 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 10 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 10 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 10 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 10 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 10 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 10 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 10 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% homologous to SEQ ID NO: 11. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% homologous to SEQ ID NO: 11. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% homologous to SEQID NO: 11.

In certain embodiments, the peptide comprises a sequence that is atleast about 80% to 99% identical to SEQ ID NO: 11. In certainembodiments, the peptide comprises a sequence that is at least about 90%to 99% identical to SEQ ID NO: 11. In certain embodiments, the peptidecomprises a sequence that is at least about 94% to 99% identical to SEQID NO: 11.

In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 11 by 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 amino acids. In certain embodiments, the peptide comprises asequence that differs from the amino acid sequence of SEQ ID NO: 11 by 1amino acid. In certain embodiments, the peptide comprises a sequencethat differs from the amino acid sequence of SEQ ID NO: 11 by 2 aminoacids. In certain embodiments, the peptide comprises a sequence thatdiffers from the amino acid sequence of SEQ ID NO: 11 by 3 amino acids.In certain embodiments, the peptide comprises a sequence that differsfrom the amino acid sequence of SEQ ID NO: 11 by 4 amino acids. Incertain embodiments, the peptide comprises a sequence that differs fromthe amino acid sequence of SEQ ID NO: 11 by 5 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 11 by 6 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 11 by 7 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 11 by 8 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 11 by 9 amino acids. In certainembodiments, the peptide comprises a sequence that differs from theamino acid sequence of SEQ ID NO: 11 by 10 amino acids.

In certain embodiments, the peptide comprises a sequence wherein any oneof the amino acids at positions 9, 10, 12, 16, 17, 20, 23, 24, 27, 28,31, or 32 of SEQ ID NO: 1 or 96 is any natural or non-natural aminoacid. In certain embodiments, the peptide comprises a sequence of SEQ IDNO: 1 or 96, wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 aminoacids at positions 9, 10, 12, 16, 17, 20, 23, 24, 27, 28, 31, or 32 canbe changed.

In certain embodiments, the peptide is a first peptide that associateswith a second peptide to form a peptide dimer that binds to a targetprotein. In certain embodiments, the peptide dimer binds to a targetprotein. In certain embodiments, the target protein is Ras. Examples ofRas include NRas, HRas, and KRas including KRas4A and KRas4B. In certainembodiments, the target protein is Ras mutant. In certain embodiments, aRas mutant is NRas, HRas, or KRas with one or more of the followingmutations: G12D, G12S, G12V, G12C, G12R, G12A, G12D, G13R, G13V, G13S,G13C, G13A, Q61L, Q61R, Q61K, or Q61H. In certain embodiments, thetarget protein is Max/Myc. In certain embodiments, the target protein isRalA. In certain embodiments, the target proteins are Ras and RalA.

In certain embodiments, the second peptide comprises the same sequenceas the sequence of the first peptide. In certain embodiments, the secondpeptide comprises a different sequence from the sequence of the firstpeptide. In certain embodiments, the second peptide comprises a sequenceof SEQ ID NO: 1 or 96. In certain embodiments, the second peptidecomprises a sequence of SEQ ID NO: 1 or 96, 12, 13, or 48. In certainembodiments, X₂₁ or X₂₅ of the second peptide is Tyr, Phe, Trp, His, oran amino acid with a cyclohexyl side chain, wherein Tyr, Phe, Trp, orcyclohexyl side chain are optionally fluorinated. In certainembodiments, X₂₁ of the second peptide is Trp. In certain embodiments,X₂₅ of the second peptide is Tyr. In certain embodiments, X₂₅ of thefirst peptide is Trp. In certain embodiments, X₂₅ of the second peptideis Tyr and X₂₅ of the first peptide is Trp. In certain embodiments, X₁₈of the second peptide is His, and each of X₂₁ and X₂₅ are Trp. Incertain embodiments, the first peptide and the second peptide areassociated through a disulfide bond, diselenide bond, carbon-carbonbond, amide bond, ester bond, hydrogen bond, salt bridge, pi stackinginteraction, or non-polar hydrophobic interaction. In certainembodiments, the first peptide and the second peptide are associatedthrough a disulfide bond or diselenium bond. In certain embodiments, twopeptides are associated through pi stacking interaction. For example, atyrosine on one peptide interacts with another tyrosine on anotherpeptide through pi stacking.

In certain embodiments, the peptides bind their target (e.g., Rasproteins) with mid-to-low nanomolar binding affinity. Without wishing tobe bound by theory, the peptides directly engage the Ras effectordomain, and block Ras from binding effector proteins necessary for itsoncogenic activity. In certain embodiments, the peptides bind Ras as ahead-to-tail dimer. In certain embodiments, the peptides bind Ras as asa head-to-tail homodimer. In certain embodiments, the peptides bind Rasas a head-to-tail heterodimer.

The binding affinity of the peptides described herein to a target (e.g.,Ras proteins) may be measured by the dissociation constant (K_(d)) of apeptide described herein and the target using methods known in the art(e.g., fluorescence polarization measurements). In certain embodiments,the peptide dimer binds Ras with a dissociation constant (K_(d)) of lessthan approximately 500 nM, 200 nM, 150 nM, 140 nM, 130 nM, 120 nM, 110nM, 100 nM, 90 nM, 80 nM, 70 nM, 60 nM, 50 nM, 40 nM, 30 nM, 20 nM, 10nM, 9 nM, 8 nM, 7 nM, 6 nM, 5 nM, 2 nM, 1 nM, or 0.5 nM. In certainembodiments, the peptide dimer binds Ras with a dissociation constant(K_(d)) of less than approximately 400 pM, 200 pM, 150 pM, 140 pM, 130pM, 120 pM, 110 pM, 100 pM, 90 pM, 80 pM, 70 pM, 60 pM, 50 pM, 40 pM, 30pM, 20 pM, 10 pM, 9 pM, 8 pM, 7 nM, 6 nM, or 5 nM. The foregoing Kavalues are applicable to both peptide homodimers and heterodimers.

In certain embodiments, the peptide dimer binds Ras with a dissociationconstant (K_(d)) of less than approximately 500 nM. In certainembodiments, the peptide dimer binds Ras with a dissociation constant(K_(d)) of less than approximately 150 nM. In certain embodiments, thepeptide dimer binds Ras with a dissociation constant (K_(d)) of lessthan approximately 150 nM. In certain embodiments, the peptide dimerbinds Ras with a dissociation constant (K_(d)) of less thanapproximately 60 nM. In certain embodiments, the peptide dimer binds Raswith a dissociation constant (K_(d)) of less than approximately 40 nM.In certain embodiments, the peptide dimer binds Ras with a dissociationconstant (K_(d)) of less than approximately 20 nM. In certainembodiments, the peptide dimer binds Ras with a dissociation constant(K_(d)) of less than approximately 10 nM. In certain embodiments, thepeptide dimer binds Ras with a dissociation constant (K_(d)) of lessthan approximately 5 nM. In certain embodiments, the peptide dimer bindsRas with a dissociation constant (K_(d)) of less than approximately 10nM. In certain embodiments, the peptide dimer binds Ras with adissociation constant (K_(d)) of less than approximately 5 nM. Incertain embodiments, the peptide dimer binds Ras with a dissociationconstant (K_(d)) of less than approximately 1 nM. In certainembodiments, the peptide dimer binds Ras with a dissociation constant(K_(d)) of less than approximately 1 nM.

In certain embodiments, the peptide dimer binds Ras with a dissociationconstant (K_(d)) of less than approximately 400 pM. In certainembodiments, the peptide dimer binds Ras with a dissociation constant(K_(d)) of less than approximately 200 pM. In certain embodiments, thepeptide dimer binds Ras with a dissociation constant (K_(d)) of lessthan approximately 150 pM. In certain embodiments, the peptide dimerbinds Ras with a dissociation constant (K_(d)) of less thanapproximately 100 pM. In certain embodiments, the peptide dimer bindsRas with a dissociation constant (K_(d)) of less than approximately 80pM. In certain embodiments, the peptide dimer binds Ras with adissociation constant (K_(d)) of less than approximately 60 pM. Incertain embodiments, the peptide dimer binds Ras with a dissociationconstant (K_(d)) of less than approximately 40 pM. In certainembodiments, the peptide dimer binds Ras with a dissociation constant(K_(d)) of less than approximately 20 pM. In certain embodiments, thepeptide dimer binds Ras with a dissociation constant (K_(d)) of lessthan approximately 10 pM. In certain embodiments, the peptide dimerbinds Ras with a dissociation constant (K_(d)) of less thanapproximately 5 pM. In certain embodiments, the peptide dimer binds Raswith a dissociation constant (K_(d)) of less than approximately 1 pM. Incertain embodiments, the peptide dimer binds Ras with a dissociationconstant (K_(d)) of less than approximately 1 pM.

In certain embodiments, the peptide dimer has a higher binding affinityfor an oncogenic form of the target protein than a non-oncogenic form.In certain embodiments, the peptide dimer has a higher binding affinityfor Ras.GTP than Ras.GDP. In certain embodiments, the peptide dimer hasa binding affinity for Ras.GTP that is greater than the binding affinityfor Ras.GDP by approximately 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, or10x.

Ras inhibition can be measured using methods such as cell viabilityassays (e.g. MTT or CellTiterGlo), caspase cleavage assays (e.g. byquantitative western blotting or Caspase 3/7 Glo), quantitative westernblotting of Ras pathway activation (e.g. activation of the MAPK pathway,PI3K/Akt pathway, Ral pathway) by measuring, for example, phosphorylatedprotein relative to total protein.

In certain embodiments, peptide monomers are a minimum of 3,000 Da and amaximum of 9,000 Da. In certain embodiments, peptide monomers are aminimum of 3,000 Da and a maximum of 6,000 Da. In certain embodiments,peptide monomers are a minimum of 6,000 Da and a maximum of 9,000 Da. Incertain embodiments, peptide dimers are a minimum of 6,000 Da and amaximum of 18,000 Da. In certain embodiments, peptide dimers are aminimum of 6,000 Da and a maximum of 12,000 Da. In certain embodiments,peptide dimerse are a minimum of 12,000 Da and a maximum of 18,000 Da.

In certain embodiments, the peptide comprises additional amino acids atthe N-terminus of SEQ ID NOs: 1-11, 96 and 99. In certain embodiments,the peptide comprises additional amino acids at the C-terminus of SEQ IDNOs: 1-11, 96 and 99. In certain embodiments, the additional amino acidscomprise X-₂G or GR at the N-terminus of SEQ ID NOs: _(1-5, 7, 96) and99. In certain embodiments, the additional amino acids comprise GCG atthe N-terminus of SEQ ID NOs: _(1-5, 7, 96) and 99. As used herein, Xwith a negative number as a subscript represents the position of anamino acid residue that is located at the N-terminal side relative to X₁of SEQ ID NO: 1 or 96.

In certain embodiments, X-₂ is an amino acid capable of cross-linkingthe first peptide with the second peptide. In certain embodiments, X-₂is an amino acid cross-linking a first peptide with a second peptide. Incertain embodiments, X-₂ is a natural or non-natural amino acid capableof cross-linking the peptide with another peptide. In certainembodiments, X-₂ is a natural or non-natural amino acid cross-linkingthe first peptide with the second peptide. In certain embodiments, X-₂is Cys, Sec, Phe, Trp, or Tyr. In certain embodiments, X-₂ is Cys. Incertain embodiments, X-₂ is Sec. In certain embodiments, X-₂ is Phe,Trp, or Tyr.

In certain embodiments, X₁₃ is Cys or Sec, and X₁₄ is Glu. In certainembodiments, X₁₈ is His, and each of X₂₅ and X₂₁ is Trp.

In certain embodiments, X₁ is Gly; each of X₃, X₄, and X₆ is Arg; and X₇is Cys. In certain embodiments, X₁ is Gly; each of X₃, X₄, and X₆ isArg; X₇ is Cy; and X₃₀is Ala. In certain embodiments, X₁ is Gly; each ofX₃, X₄, and X₆ is Arg; X₇ is Cys; and X₃₀is Arg. In certain embodiments,X-₂ is Gly; X-₁ is Arg; X₁ is Arg; each of X₃, X₄, and X₆ is Arg; X₇ isCys; and X₃₀is Ala. In each of the foregoing embodiments, it is alsocomtemplated that Sec is used in place of Cys.

In certain embodiments, a heterodimerized peptide comprises a primarypeptide and a secondary peptide. The primary peptide forms a majority ofcontacts to Ras.

In certain embodiments, a heterodimerized peptide comprises a primarypeptide selected from SEQ ID NO: 22, 23, and 49. In certain embodiments,a heterodimerized peptide comprises a secondary peptide selected fromSEQ ID NO: 24-27, 50, and 51. In certain embodiments, a heterodimerizedpeptide comprises a primary peptide of SEQ ID NO: 22 and and a secondarypeptide of SEQ ID NO: 24. In certain embodiments, a heterodimerizedpeptide comprises a primary peptide selected from SEQ ID NO: 22 and asecondary peptide of SEQ ID NO: 25. In certain embodiments, aheterodimerized peptide comprises a primary peptide of SEQ ID NO: 22 andand a secondary peptide of SEQ ID NO: 26. In certain embodiments, aheterodimerized peptide comprises a primary peptide of SEQ ID NO: 22 andand a secondary peptide of SEQ ID NO: 27. In certain embodiments, aheterodimerized peptide comprises a primary peptide of SEQ ID NO: 22 andand a secondary peptide of SEQ ID NO: 50. In certain embodiments, aheterodimerized peptide comprises a primary peptide of SEQ ID NO: 22 andand a secondary peptide of SEQ ID NO: 51.

In certain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 23 and a secondary peptide of SEQ ID NO: 24. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 23 and a secondary peptide of SEQ ID NO: 25. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 23 and a secondary peptide of SEQ ID NO: 26.

In certain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 23 and a secondary peptide of SEQ ID NO: 27. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 23 and and a secondary peptide of SEQ ID NO: 50.In certain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 23 and and a secondary peptide of SEQ ID NO: 51.

In certain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 49 and a secondary peptide of SEQ ID NO: 24. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 49 and a secondary peptide of SEQ ID NO: 25. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 49 and a secondary peptide of SEQ ID NO: 26. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 49 and a secondary peptide of SEQ ID NO: 27. Incertain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 49 and and a secondary peptide of SEQ ID NO: 50.In certain embodiments, a heterodimerized peptide comprises a primarypeptide of SEQ ID NO: 49 and and a secondary peptide of SEQ ID NO: 51.

In one aspect, provided herein are peptides designed to prevent orminimize dimerization prior to cell penetration. The peptides disclosedherein can comprise masked Cys or Sec. Prior to cell penetration,cysteine or selenocysteine residues in a peptide monomer can bedisulfide bonded or selenium-sulfide bonded to a small organic thiolmoieties to prevent crosslinking because sulfur in disulfide form or inselenium-sulfide form are not nucleophilic. In certain embodiments, apeptide monomer comprises a cysteine that is disulfide bonded to a smallorganic thiol moiety. In certain embodiments, a peptide monomercomprises a selenocysteine that is selenium-sulfide bonded to a smallorganic thiol moiety. In certain embodiments, the small organic thiolmoiety is an aliphatic thiol moiety. In certain embodiments, thealiphatic thiol is an alkyl thiol moiety. In certain embodiments, thealkyl thiol is a C₁₋₅ alkyl thiol. In certain embodiments, the smallorganic thiol moiety is SR^(S), wherein R^(S) is a substituted orunsubstituted C₁₋₅ alkyl. In certain embodiments, R^(S) is a substitutedC₁₋₅ alkyl. In certain embodiments, R^(S) is an unsubstituted C₁₋₅alkyl. In certain embodiments, the small organic thiol moiety is t-butylthiol. In certain embodiments, the small organic thiol moiety isethanethiol. The inventive peptides described herein which are monomericcan comprise Cys that are either not disulfide bonded or Cys that aredisulfide bonded. In certain embodiments, the inventive peptides aremonomers comprising a Cys that is not disulfide bonded. In certainembodiments, the inventive peptides are monomers comprising a Cys thatis disulfide bonded. In certain embodiments, the peptide comprises asequence selected from the group consisting of SEQ ID NO: 30, 33, and34, wherein the Cys is not disulfide bonded. In certain embodiments, thepeptide comprises a sequence selected from the group consisting of SEQID NO: 30, 33, and 34, wherein the Cys is disulfide bonded to smallorganic thiol moieties. In any of the foregoing embodiments, Sec is alsocontemplated in place of Cys.

Following cell penetration, the disulfide bonded cysteines of thepeptide monomers are reduced in the cytoplasm environment, allowing thefree thiol of the cysteine residues to crosslink to a second peptidemonomer comprising an electrophilic side chain that can react with thethiol nucleophile. This strategy is also applicable to peptidescomprising selenocysteines, which can serve as the nucleophile forcrosslinking. For example, electrophilic side chains include those withacrylamide, vinyl sulfonamide, iodoacetamide moieties. Other Michaelacceptors capable of reacting with Cys or Sec are also applicable forcrosslinking the peptides and are known in the art. For example, thepeptides can contain residues modified with moieties capable ofcrosslinking to Cys or Sec. For example, amino acid side chainscomprising an acrylamide moiety. In certain embodiments, the peptidescomprise an amino acid sidechain containing an acrylamide moiety. Incertain embodiments, the peptides comprise L-2,4-diaminobutyric acid(Dab) residues or L-2,3-diaminopropionic acid (Dap) residues. As usedherein, residue X is a L-2,4-diaminobutyric acid (Dab) residue andresidue Z is a L-2,3-diaminopropionic acid (Dap) residue.

In certain embodiments, the Dab or Dap residues have acrylic acidcoupled to the side chain nitrogen to form an acrylamide side chain witheither 1 or 2 carbons separating the acrylamide from the peptidebackbone alpha carbon. Side chains for Dap and Dab residues coupled toacrylic acid to form a side chain with an acrylamide are shown below.Such Dap or Dab-modified residues are referred to as Dab- andDap-conjugated acrylamide residues.

In certain embodiments, the peptide comprises a sequence selected fromthe group consisting of SEQ ID NO: 31, 32, 35, and 36, wherein X₁₈L-2,4-diaminobutyric acid (Dab) residue or wherein Z is aL-2,3-diaminopropionic acid (Dap) residue conjugated to acrylamide.

In certain embodiments, peptides comprising a L-2,4-diaminobutyric acid(Dab) residue or L-2,3-diaminopropionic acid (Dap) residue are coupledwith acrylic acid to the side chain nitrogen of Dap or Dab to form aside chain comprising an acrylamide.

Peptide dimers can be formed from any combination of SEQ ID NO: 30, 33,and 34 with SEQ ID NO: 31, 32, 35, and 36.

Provided herein are also selective dimer destabilization strategies.Destabilizing the dimer in endosomes can improve endosomal escape andtherefore cytosolic access of the dimer. Monomers are thought to be moreefficient at escaping endosomes compared to dimers. Dimerdestabilization can be pH-induced or induced with bulky residues.pH-induced dimer destabilization involves placing histidines residuesinto one peptide monomer such that they are spatially close to cationicresidues or other histidines on the opposing monomer. At regularcytosolic pH (˜7.4) these histidines are less positively charged than inendosomes (pH˜5-6), and thus the dimer is selectively destabilized inendosomes, thus leading to more efficient escape. Histidine's pKa of6.0 - 6.5 causes it to be largely neutral at cytosolic pH values (pH7.2 - 7.4), but results in protonation in the endosomes, which typicallybegin around pH 6.0 and progress to pH 5.0 or lower as the endosometransitions to a lysosome. The placement of histidine residues nearpositive charges on the opposing monomer leads to electrostaticrepulsion between the two peptide monomers upon entry into the endosome,which destabilizes the dimer, favoring the monomer state.

SEQ ID NO: 38-41 illustrate this histidine pH-induced destabilizationstrategy. In certain embodiments, the peptide comprises a sequencewherein the His are placed at positions X₆, X₇, and/or X₁₀. His placedat one, two, or three of these positions is applicable to any of thepeptides described herein. In certain embodiments, the peptide comprisesa sequence selected from the group consisting of SEQ ID NO: 38 to 41.FIGS. 36A-B compare cells containing the same concentration of SEQ IDNO: 37, which does not contain histidines, and SEQ ID NO: 38, whichcontains histidines, using live-cell microscopy.

Dimer destabilization can also be achieved using residues comprisingbulky moieties near the dimer interface to prevent dimerization. Uponentry into the cell, the bulky moieties of the residues are removed,permitting dimerization and binding to a protein target such as Ras,Myc/Max, or RalA. This strategy is applicable to any peptides describedherein comprising Cys or Sec. In certain embodiments, the peptidecomprises Cys or Sec protected by a thiol molecule. For example, aninventive peptide described herein comprises a Cys or Sec at a certainposition (e.g., X₇) and is protected by disulfide bonding to an organicthiol, e.g., by reacting the reduced thiol with 2,2′-dipyridyldisulfide,4,4′-dipyridyldisulfide, 2,2′-dithiobis(5-nitropyridine), or similarreagents. In certain embodiments, the peptide comprises Cys or Secprotected by bonding to an organic thiol molecule. In certainembodiments, the organic thiol molecule is an aryl thiol, heteroaylthiol, or an aliphatic thiol. In certain embodiments, the organic thiolmolecule is a heteroaryl thiol. In certain embodiments, the organicthiol molecule is selected from 2,2′-dipyridyldisulfide,4,4′-dipyridyldisulfide, and 2,2′-dithiobis(5-nitropyridine). In certainembodiments, the peptide comprises Sec protected with the reagent2,2′-dithiobis(5-nitropyridine). Upon escape from endosomes into thecytosol, this disulfide bond would be reduced by cell's environment anddimerization would be permitted. In certain embodiments, the peptidecomprises Cys protected by disulfide bonding to 2,2′-Dipyridyldisulfide.In certain embodiments, the peptide comprises Cys protected by disulfidebonding to 4,4′-dipyridyldisulfide. In certain embodiments, the peptidecomprises Cys protected by disulfide bonding to2,2′-dithiobis(5-nitropyridine). Sequences demonstrating this strategyinclude SEQ ID NO: 30, 33, 34, and 42. It is understood that Cys can bereplaced with Sec in any of the embodiments described herein.

As previously discussed, other targets besides Ras are contemplated. SEQID NO: 43 binds the Myc/Max heterodimer. SEQ ID NO: 44 binds the RalAprotein. SEQ ID NO: 45 binds both RalA and KRas. SEQ ID NO: 43-45 arepeptides comprising Cys at position 7, which dimerizes using disulfidebonds.

Further provided herein are peptides comprising a oligomerization domainthat allows the peptide to associate with another peptide to form adimer, wherein the oligomerization domain comprises a sequence:PX_(a)X_(b)PX_(c)X_(d)P (SEQ ID NO: 2), wherein each of X_(a), X_(b),and X_(c) is any non-proline amino acid, and X_(d) is an amino acidcapable of cross-linking the peptide with another peptide. In certainembodiments, each of X_(a) and X_(b) is independently any non-prolineamino acid, and each of X_(c) and X_(d) is independently any non-prolineamino acid or an amino acid capable of cross-linking the peptide withanother peptide (e.g., cysteine, selenocysteine). In certainembodiments, each of X_(c) and X_(d) is independently any non-prolineamino acid but each is not an amino acid capable of cross-linking thepeptide with another peptide. The peptides comprising a oligomerizationdomain are useful as inhibitors of protein-protein interactions. Thepeptides comprising a oligomerization domain are useful for binding andinhibiting a target protein such as Ras or a Ras mutant.

In certain embodiments, the cross-linking amino acid in the firstpeptide of the dimer forms a cross-link to the accompanyingcross-linking amino acid in the second peptide's PX_(a)X_(b)PX_(c)X_(d)Pmotif. In certain embodiments, the PX_(a)X_(b)PX_(c)X_(d)P motifs in thefirst and second peptides are in an antiparallel configuration. Incertain embodiments, the PX_(a)X_(b)PX_(c)X_(d)P motif adopts a PPIIhelical configuration. In certain embodiments, thePX_(a)X_(b)PX_(c)X_(d)P motifs would each be connected to an alpha helixat either their N- or C-termini and would stabilize the alpha helices inan antiparallel configuration.

In certain embodiments, X_(c) is Cys, Sec, Phe, Trp, or Tyr. In certainembodiments, X_(c) is an amino acid capable of cross-linking the peptidewith another peptide. In certain embodiments, X_(c) is Cys or Sec. Incertain embodiments, X_(c) is Cys. In certain embodiments, X_(c) is Sec.

In certain embodiments, X_(d) is Cys, Sec, Phe, Trp, or Tyr. In certainembodiments, X_(d) is an amino acid capable of cross-linking the peptidewith another peptide. In certain embodiments, X_(d) is Cys or Sec. Incertain embodiments, X_(d) is Cys. In certain embodiments, X_(d) is Sec.

In certain embodiments, when X_(c) is an amino acid capable ofcross-linking the peptide with another peptide, X_(d) is not an aminoacid capable of cross-linking the peptide with another peptide. Incertain embodiments, when X_(d) is an amino acid capable ofcross-linking the peptide with another peptide, X_(c) is not an aminoacid capable of cross-linking the peptide with another peptide.

In certain embodiments, the peptides comprise SEQ ID NO: 2 or 99,wherein X_(a) and X_(b) are each Arg. In certain embodiments, thepeptides comprise SEQ ID NO: 2 or 99, wherein X_(c) is Arg, and X_(d) isCys. In certain embodiments, the peptides comprise SEQ ID NO: 2 or 99,wherein X_(c) is Arg, and X_(d) is Tyr. In certain embodiments, thepeptides comprise SEQ ID NO: 2 or 99, wherein X_(c) is Lys, and X_(d) isTyr. In certain embodiments, the peptides comprise SEQ ID NO: 2 or 99,wherein X_(c) is Cys, and X_(d) is Tyr. In certain embodiments, thepeptides comprise SEQ ID NO: 2 or 99, wherein X_(c) is Lys, and X_(d) isCys. In certain embodiments, the peptides comprise SEQ ID NO: 2 or 99,wherein X_(c) is Lys, and X_(d) is His. In certain embodiments, thepeptides comprise SEQ ID NO: 2 or 99, wherein X_(c) is Arg, and X_(d) isHis. In certain embodiments, the peptides comprise SEQ ID NO: 2 or 99,wherein X_(c) is His, and X_(d) is His. In certain embodiments, thepeptides comprise SEQ ID NO: 2 or 99, wherein X_(c) is His, and X_(d) isTyr. In certain embodiments, the peptides comprise SEQ ID NO: 2 or 99,wherein X_(a) and X_(b) are each Arg and each of X_(c) and X_(d) haveany of the foregoing general and specific embodiments.

In any of the embodiments of SEQ ID NO: 2 or 99, X_(a), X_(b), X_(c),and X_(d) corresponds to X₃, X₄, X₆, and X₇, respectively, as describedherein.

The peptide further comprises an alpha-helical domain comprising asequence: X₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA (SEQ ID NO: 3),wherein X₁₃, X₁₄, X₁₅, X₁₈, X₁₉, X₂₁, X₂₂, X₂₅, X₂₆, X₂₉, and X₃₀ are asdefined herein.

Further provided herein are peptides comprising an alpha-helical domaincomprising a sequence: X₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA (SEQID NO: 3), wherein X₁₃, X₁₄, X₁₅, X₁₈, X₁₉, X₂₁, X₂₂, X₂₅, X₂₆, X₂₉, andX₃₀ are as defined herein.

In certain embodiments, the inventive peptides are soluble in aqueousmedia. In certain embodiments, the inventive peptides can penetratecells. In certain embodiments, the peptides comprise a reduced number ofnegative charges. In certain embodiments, the number of negative chargesof a peptide is reduced by 1, 2, 3, 4, 5, or 6 negative charges comparedto the starting peptide. For example, introducing Ala or Ser in place ofanionic residues can help to increase cell penetration. In certainembodiments, the disclosed peptides comprise at least one, two, or threenon-negatively charged amino acids at positions X₁₁, X₁₅, and/or X₁₆. Incertain embodiments, the disclosed peptides comprise at least one, two,three, or four non-negatively charged amino acids at positions X₁₁, X₁₅,X₁₆, and/or X₁₉. In certain embodiments, the disclosed peptides comprisefour non-negatively charged amino acids at positions X₁₁, X₁₅, X₁₆, andX₁₉. In certain embodiments, the non-negatively charged amino acids areneutral amino acids. In certain embodiments, the non-negatively chargedamino acids are selected from the group consisting of Ala, Val, Leu,Ile, Pro, Phe, Trp, Met, Gly, Ser, Thr, Cys, Tyr, Asn, and Gln. Incertain embodiments, the non-negatively charged amino acids arepositively charged amino acids. In certain embodiments, the positivelycharged amino acids are selected from the group consisting of Lys, Arg,and His. In certain embodiments, the peptides comprise Ala at amino acidpositions X₁₁, X₁₅, X₁₆, and X₁₉.

In certain embodiments, the disclosed peptides comprise at least one,two, three, or four Ala and/or Ser at positions X₁₁, X₁₅, X₁₆, and/orX₁₉. In certain embodiments, the disclosed peptides comprise at leastone, two, or three Ala at positions X₁₁, X₁₅, and/or X₁₆. In certainembodiments, the disclosed peptides comprise at least one, two, three,or four Ala at positions X₁₁, X₁₅, X₁₆, and/or X₁₉. In certainembodiments, the disclosed peptides comprise Ala at positions X₁₁, X₁₅,X₁₆, and X₁₉. The foregoing embodiments for Ala at positions X₁₁, X₁₅,and/or X₁₆ are also applicable to Ser at positions X₁₁, X₁₅, and/or X₁₆.

Methods of Preparing the Inventive Peptides

The synthesis of the inventive peptides first involves the selection ofa desired sequence and number of amino acids including unnatural aminoacids. Once the amino acids are selected, synthesis of the inventivepeptides can be achieved using standard deprotection and couplingreactions. Formation of peptide bonds and polypeptide synthesis aretechniques well-known to one skilled in the art, and encompass bothsolid phase and solution phase methods; see generally, Bodanszky andBodanszky, The Practice of Peptide Synthesis, Springer-Verlag, Berlin,1984; Atherton and Sheppard, Solid Phase Peptide Synthesis: A PracticalApproach, IRL Press at Oxford University Press Oxford, England, 1989,and Stewart and Young, Solid phase Peptide Synthesis, 2nd edition,Pierce Chemical Company, Rockford, 1984, the entire contents of each ofwhich are incorporated herein by reference. In both solution phase andsolid phase techniques, the choice of the protecting groups must beconsidered, as well as the specific coupling techniques to be utilized.For a detailed discussion of peptide synthesis techniques for solutionphase and solid phase reactions, see, Hecht, Bioorganic chemistry:Peptides and Proteins, Oxford University Press, New York: 1998, theentire contents of which are incorporated herein by reference.

In certain embodiments, the methods comprises associating the inventivestapled peptides by ligating it to another polypeptide or a proteinfollowing the strategies as described in US Publication No. US2012/0270800 and International Application No. PCT/US2010/001952, whichare also incorporated herein by reference. In certain embodiments, theother polypeptide to be ligated is stapled or stitched.

In certain embodiments, the method comprises a solution phase synthesisof the inventive peptides. Solution phase synthesis, as mentioned above,is a well-known technique for the construction of polypeptides. Anexemplary solution phase synthesis comprises the steps of: (1) providingan amino acid protected at the N-terminus with an amino protectinggroup; (2) providing an amino acid protected at the C-terminus with anoxygen protecting group; (3) coupling the N-protected amino acid to theC-protected amino acid; (4) deprotecting the product of the couplingreaction either at the N-terminus or C-terminus; and (5) repeating steps(3) to (4) until a desired polypeptide is obtained, wherein at least twoof the amino acids coupled at any of the above steps each comprise atleast one terminally unsaturated amino acid sidechain, and, optionally,an amino acid comprising two terminally unsaturated amino acid sidechains. During the course of the above synthesis, various parameters canbe varied, including, but not limited to, stereochemistry of aminoacids, and amino acid residues utilized.

In certain embodiments, the method comprises a solid phase synthesis ofthe inventive peptides. Solid phase synthesis, as mentioned above, is awell-known technique for the construction of polypeptides. An exemplarysolid phase synthesis includes the steps of: (1) providing a resin—boundamino acid; (2) deprotecting the resin bound amino acid; (3) coupling anamino acid to the deprotected resin-bound amino acid; (4) repeatingsteps (3) until a desired peptide is obtained.

During the course of the above synthesis, various parameters can bevaried, including, but not limited to placement of amino acids with sidechains, stereochemistry of amino acids, side chain length andfunctionality, and amino acid residues utilized.

In certain embodiments, the synthesized peptide contains amino acidcapable of cross-linking the peptide with another peptide. For example,the amino acid can enable the peptide to be stapled when contacted witha specific catalyst to promote the stapling, or multiple stapling, toprovide a stapled version of the peptide to provide a conformationallystabilized peptide. Such amino acids include those with terminallyunsaturated amino acid side chains.

Other modifications may include conjugation of the peptides with a cellpermeating agent, therapeutically active agent, label, or diagnosticagent anywhere on the peptide scaffold, e.g., such as at the N-terminusof the peptide, the C-terminus of the peptide, on an amino acid sidechain of the peptide. Such modification may be useful in delivery of thepeptide or therapeutically active agent to a cell, tissue, or organ.Such modifications may, in certain embodiments, allow for targeting to aparticular type of cell or tissue.

In certain embodiments, one or more of the amino acids in a peptide maybe modified, for example, by the addition of a chemical entity such as acarbohydrate group, a hydroxyl group, a phosphate group, a farnesylgroup, an isofarnesyl group, palmitoyl, geranylgeranyl, lauryl, a fattyacid group, a linker for conjugation, functionalization, or othermodification. Use of lipids can help the peptides localize to the plasmamembrane, where Ras is localized.

In certain embodiments, the inventive peptides comprises D-amino acids.In certain embodiments, the inventive peptides comprise up to 10%D-amino acids. In certain embodiments, the inventive peptides compriseup to 20% D-amino acids. In certain embodiments, the inventive peptidescomprise up to 30% D-amino acids. In certain embodiments, the inventivepeptides comprise up to 40% D-amino acids. In certain embodiments, theinventive peptides comprise up to 50% D-amino acids. In certainembodiments, the inventive peptides comprise up to 60% D-amino acids. Incertain embodiments, the inventive peptides comprise up to 70% D-aminoacids. In certain embodiments, the inventive peptides comprise up to 80%D-amino acids. In certain embodiments, the inventive peptides compriseup to 90% D-amino acids.

In certain embodiments, the inventive peptides are entirely D-aminoacids. Such “mirror image” proteins can fold into the correspondingmirror image conformation and is expected to have the samePPII-loop-alpha helix conformation, as well as the ability to dimerize(and crosslink via a disulfide or diselinide at the aforementionedpositions) as an inventive peptide comprising L-amino acids. In certainembodiments, computational methods are used to discover binders totargets. In certain embodiments, “mirror image display” technologieswhere yeast, phage, etc. display is used with D-amino acid targetproteins. In certain embodiments, Ras-binding peptides disclosed hereindo not comprise D-amino acids.

Peptide Conjugation to Other Peptides or to Stapled or Stitched Peptides

The peptides described herein can be conjugated to another peptide whichare stapled to stitched or to another peptide that are cell-penetratingpeptides (e.g., TAT). Stapled or stitched peptide or cell-penetratingpeptides allow the peptides provided herein to permeate cells. Stapledor stitched peptides have been described in, for example, Walensky etal., Science (2004) 305:1466-1470; U.S. Pat. Nos. 8,592,377; 7,192,713;U.S. Patent Application Publication No. 2006/0008848; U.S. PatentApplication Publication No. 2012/0270800; International Publication No.WO 2008/121767 and International Publication No. WO 2011/008260, each ofwhich are incorporated herein by reference. Cell-penetrating peptidesare described in, for example, Margus, et al., Cell-penetrating peptidesas versatile vehicles for oligonucleotide delivery. Mol Ther. (2012);20(3):525-33

Dimer Display Technology

The methods of screening provided herein can be used with various invitro display methods. A method of high-throughput screening is usefulfor identifying peptides that bind a target protein. A number of methodsexist for preparing and evaluating large numbers of proteins (orpeptides) for binding activity, which are collectively referred to as“display” technologies. Most of these technologies rely on biosynthesismachinery (i.e., ribosomes, either in a cell or in vitro) to synthesizethe proteins based on a DNA template encoding their sequence, and somemeans of physically linking the expressed protein to the DNA encodingit. This latter feature provides a ready means of determining theidentity of the proteins that are selected for their activity using PCRand well-established DNA sequencing technology, which enables theamplification and analysis of even single molecules of DNA. Onceproteins are expressed and linked to their encoding DNA, those with thedesired properties can be isolated from the rest using a variety oftechniques, which are generally either a “screen” (in which eachindividual species is evaluated one-by-one) or a “selection” (in whichthe molecules are evaluated in bulk). Display technologies can be usedboth to identify binding agents from naïve libraries, and to improve theproperties of proteins that already possess the desired activity. Thislatter method, which typically involves preparing mutant libraries ofthe original protein, isolating the best variants, and repeating thesesteps, is referred to as “directed evolution.” Directed evolution hasbeen reviewed, for example, in Dougherty and Arnold, Directed evolution:new parts and optimized function. Curr Opin Biotechnol. (2009);20(4):486-91.

One exemplary display technique is phage display, which involvesexpressing proteins of interest as a fusion to a coat protein from theM13 phage. Large libraries of phage can be prepared by transforming theappropriate library DNA into E. coli, and once produced, the activemembers of the library can be isolated, typically through a “panning”selection in which a target binding protein is immobilized and the phageare washed over the surface to bind the active variants. Phage displayis the most commonly used display technology and has been used toidentify proteins and peptides that bind a wide variety of biologicaland nonbiological targets (Levin, A. M. and Weiss, G. A. Optimizing theaffinity and specificity of proteins with molecular display. Mol Biosyst2, 49-57 (2006)).

Yeast surface display is further described in Boder and Wittrup, Yeastsurface display for screening combinatorial polypeptide libraries, NatBiotechnol 15, 553-7 (1997) and in U.S. Pat. No. 6,300,065. Generally,the yeast surface display method involves transforming a DNA libraryinto cells (such as S. cerevisiae), in which the displayed proteins arefused to a yeast surface protein, Aga2p (FIG. 2 ). Yeast cells are largeenough to enable screening by fluorescence-activated cell sorting(FACS), which can evaluate >10⁷ cells per hour and is capable of sortingcells based on multiple fluorescent signals. This permits multiparametersorting, allowing cells to be selected not based solely on theirabsolute binding (e.g., to a fluorescently labeled target protein) butbased on ratios of different fluorophores. This enables cell selectionsthat may not possible with some other display cells such as phages; forexample, the target binding signal can be normalized to expression levelif a labeled antibody to an epitope on the fusion protein is used, orcells can be selected based on their preference for one labeled targetprotein over a differently labeled target. Normalization to expressionis particularly useful as it is not possible with phage, which oftenpossess strong expression biases for displayed proteins.

An additional feature of yeast display is that the displayed proteinspass through the yeast secretory system, which facilitates the formationof disulfide bonds (and folding in general, relative to E. coli). Thisfeature is advantageous for proteins that require properly-formeddisulfide bonds for activity; although some disulfide-containingproteins and peptides have been successfully displayed on phage, manyare unable to be properly formed.

In addition to yeast surface display, an analogous bacterial system hasbeen developed that displays proteins as fusions to a cell surfaceprotein. Although this method possesses some of the advantages of yeastsurface display, and in principle can achieve higher library sizes thanyeast (although smaller than phage), it does not possess the folding anddisulfide formation capabilities of the yeast system. Finally, there area number of in vitro display methods, which involve generating DNAtemplates and producing proteins in cell-free translation extracts.These methods can accommodate the highest theoretical library sizes, astransformation is not required, and can often detect the activity ofsingle sequences, as PCR is typically used to amplify isolated hits. Incertain embodiments, mRNA display or ribosome display can be used todisplay the peptide libraries.

Provided herein are methods of screening a library of peptide dimers.The methods comprises transforming display cells with a vector encodinga first peptide and a second peptide, wherein the first and secondpeptides associate to form a peptide dimer fused to a cell wall protein;contacting the display cells with a first label, wherein the first labelcomprises a target protein and associates with a cell expressing thepeptide dimer having enhanced binding to the target and does notassociate with a cell which does not express the peptide dimer havingenhanced binding to the target; isolating the display cells with whichthe first label is associated; and identifying the first and secondpeptides which exhibit enhanced binding to the target. Alternatively,the method can comprise transforming display cells with a first vectorencoding a first peptide and second vector encoding a second peptide.

Peptide libraries can be generated using methods such as PCR (see FIG. 5). For example, random mutagenesis (error-prone PCR) of a templatesequence can be used. A set of primers with sufficient overlap areannealed to a template and extended, thereby serving as templates forone another. Mutations are introduced through the use of multipledegenerate codons within each primer (site saturation mutagenesis),providing high combinatorial diversity in the resulting library. Anotherway to generate libraries is to start with a defined mixture of a numberof codons (one for each amino acid) that are incorporated into theprimer with a mixture of trimer phosphoroamidites during the primersynthesis.

The peptide libraries can be designed from any peptide based on thepancreatic polypeptide family. In certain embodiments, the peptides usedto design the libraries are based on avian, human, bovine, ovine,porcine, canine pancreatic polypeptides or mutants thereof. In certainembodiments, the peptides used to design the libraries are based onavian pancreatic polypeptide (aPP) or mutants thereof The peptidelibraries can be designed from any peptide comprising a scaffold of thepancreatic polypeptide family. The peptide libraries can be designedfrom any peptide comprising PPII helix domain and an alpha-helicaldomain. The peptide libraries can be designed from any peptidecomprising PPII helix domain, a loop domain, and an alpha-helicaldomain. In certain embodiments, the loop domain is a type-I beta-turn.In certain embodiments, the peptides used to design the libraries arebased on SEQ ID NO: 1 or 96 or 4-11. In certain embodiments, thepeptides used to design the libraries are based on SEQ ID NO: 1 or 96.In certain embodiments, the peptide libraries can be designed from anypeptide with 80% to 99% homology to SED ID NO: 1 or 96 or 4-11. Incertain embodiments, the peptide libraries can be designed from anypeptide with 80% to 99% identify to SED ID NO: 1 or 96 or 4-11. Incertain embodiments, the peptide libraries can be designed from anypeptide comprising SEQ ID NO: 2 or 99. In certain embodiments, thepeptide libraries can be designed from any peptide comprising SEQ ID NO:3.

In certain embodiments, the inventive peptides/dimers as describedherein is a peptide homodimer of two peptides each comprising analpha-helical structure. In certain embodiments, the inventivepeptides/dimers as described herein is a peptide homodimer of twopeptides each comprising a polyproline type-II conformation. In certainembodiments, the inventive peptides/dimers as described herein is apeptide homodimer of two peptides each comprising an alpha-helicalstructure connected to polyproline type-II conformation by a loopdomain. In certain embodiments, the loop/linker domain is a type-Ibeta-turn. In certain embodiments, the inventive peptides/dimers asdescribed herein is a peptide heterodimer of two peptides eachcomprising an alpha-helical structure. In certain embodiments, theinventive peptides/dimers as described herein is a peptide heterodimerof two peptides each comprising a polyproline type-II conformation. Incertain embodiments, the inventive peptides/dimers as described hereinis a peptide heterodimer of two peptides each comprising analpha-helical structure connected to polyproline type-II conformation bya loop.

In certain embodiments, the two peptides are bound covalently. Incertain embodiments, the two peptides are bound non-covalently. Incertain embodiments, two peptides are associated through a disulfidebond, diselenium bond, carbon-carbon bond, amide bond, ester bond,hydrogen bond, salt bridge, pi stacking interaction, or non-polarhydrophobic interaction. In certain embodiments, two peptides areassociated through a disulfide bond. In certain embodiments, twopeptides are associated through a diselenium bond. In certainembodiments, two peptides are associated through a hydrogen bond, saltbridge, or non-polar hydrophobic interaction. In certain embodiments,two peptides are associated through pi stacking interaction. Forexample, a tyrosine on one peptide interacts with another tyrosine onanother peptide through pi stacking.

In certain embodiments, each of the two peptides independently comprisesthe sequence of SEQ ID NO: 1 to SEQ ID NO: 11 or sequences thereof whichare at least approximately 80%, 85%, 90%, 95%, 98%, or 99% homologous oridentical. In certain embodiments, each of the two peptides comprise amoiety that is an amino acid capable of cross-linking the peptide withanother peptide. In certain embodiments, each of the two peptidescomprise a moiety cross-linking the two peptides to one another. Incertain embodiments, the amino acid capable of cross-linking is Cys orSec.

In certain embodiments, the moiety capable of cross-linking is anon-natural amino acid capable of cross-linking the first peptide withthe second peptide. In certain embodiments, the display cells aremammalian cells, bacterial cells, or phages. In certain embodiments, thedisplay cells are yeast cells. In certain embodiments, the display cellsare S. cerevisiae. In certain embodiments, the peptide dimers are fusedto a yeast surface protein. In certain embodiments, the yeast surfaceprotein is Aga2p.

In certain embodiments, the target protein is asymmetric. In certainembodiments, the target protein is Ras or a Ras mutant. In certainembodiments, the peptides possess a higher selectivity for Ras.GTP thanRas.GDP. In certain embodiments, the peptides are at least approximately1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, or 10x more selective for Ras.GTPthan Ras.GDP.

The first label is used to label the target protein and is thenincubated with the display cells. In certain embodiments, the firstlabel is a fluorescent label bound to a target protein. In certainembodiments, the first label is biotin bound to Ras. Other fluorophorescan be used to label the target protein such as phycoerythrin,allophycocyanin, Alexa647, Alexa488, and FITC.

An optional second label can be used to measure the abundance of thedisplayed fusion protein on the display cell. The second label can be anantibody that is fluorescently labeled or microbeads capable of bindingthe first label. Exemplary methods useful for sorting the display cellscontaining the bound target protein include fluorescent activated cellsorting (FACS) and magnetic-activated cell sorting (MACS).

Methods of Use and Treatment

Provided herein are methods of treating a disease or conditionassociated with Ras in a subject in need thereof comprisingadministering an effective amount of a peptide as described herein tothe subject. Provided herein are methods of treating a disease orcondition associated with Ras in a subject in need thereof comprisinginstructing the subject to take an effective amount of a peptide asdescribed herein to the subject. Also provided herein are peptides foruse in treating a disease or condition associated with Ras in a subjectin need thereof

In certain embodiments, the disease associated with Ras is aproliferative disease. As used herein a proliferative disease,condition, or disorder includes, but is not limited to, cancer,hematopoietic neoplastic disorders, benign neoplasms (i.e., tumors),diabetic retinopathy, rheumatoid arthritis, macular degeneration,obesity, and atherosclerosis. In certain embodiments, the proliferativedisease is cancer. Exemplary cancers include, but are not limited to,carcinoma, sarcoma, or metastatic disorders, breast cancer, ovariancancer, colon cancer, lung cancer, fibrosarcoma, myosarcoma,liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma,endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma,synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma,rhabdomyosarcoma, gastric cancer, esophageal cancer, rectal cancer,pancreatic cancer, ovarian cancer, prostate cancer, uterine cancer,cancer of the head and neck, skin cancer, brain cancer, stomach cancer,squamous cell carcinoma, sebaceous gland carcinoma, papillary carcinoma,papillary adenocarcinoma, cystadenocarcinoma, medullary carcinoma,bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile ductcarcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor,cervical cancer, testicular cancer, small cell lung carcinoma, non—smallcell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma,astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma,hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma,melanoma, neuroblastoma, retinoblastoma, leukemia, lymphoma, andKaposi's sarcoma.

Exemplary hematopoietic neoplastic disorders include, but are notlimited to, disorders involving hyperplastic/neoplastic cells ofhematopoietic origin, e.g., arising from myeloid, lymphoid or erythroidlineages, or precursor cells thereof. In certain embodiments, thedisorders arise from poorly differentiated acute leukemias, e.g.,erythroblastic leukemia and acute megakaryoblastic leukemia. Additionalexemplary myeloid disorders include, but are not limited to, acutepromyeloid leukemia (APML), acute myelogenous leukemia (AML) and chronicmyelogenous leukemia (CML); lymphoid malignancies include, but are notlimited to acute lymphoblastic leukemia (ALL) which includes B—lineageALL and T-lineage ALL, chronic lymphocytic leukemia (CLL),prolymphocytic leukemia (PLL), hairy cell leukemia (HLL) andWaldenstrom's macroglobulinemia (WM). Additional forms of malignantlymphomas include, but are not limited to non—Hodgkin lymphoma andvariants thereof, peripheral T-cell lymphomas, adult T cellleukemia/lymphoma (ATL), cutaneous T-cell lymphoma (CTCL), largegranular lymphocytic leukemia (LGF), Hodgkin's disease, andReed-Stemberg disease.

In certain embodiments, the disease associated with Ras is anon-proliferative disease. In certain embodiments, the diseaseassociated with Ras is a RASopathy. In certain embodiments, the diseaseassociated with Ras is CFC syndrome, capillarymalformation-arteriovenous malformation syndrome, Costello syndrome,Legius syndrome, Neurofibromatosis type 1, Noonan syndrome, or Noonansyndrome with multiple lentigines (formerly LEOPARD syndrome).

Pharmaceutical Compositions

Provided herein are pharmaceutical compositions comprising a peptide asdescribed herein and a pharmaceutically acceptable excipient.Pharmaceutical compositions comprise compositions for therapeutic use.Such compositions may optionally comprise one or more additionaltherapeutically active agents. In accordance with some embodiments, amethod of administering a pharmaceutical composition comprising aninventive composition to a subject in need thereof is provided. In someembodiments, the inventive composition is administered to humans. Forthe purposes of the present invention, the “active ingredient” generallyrefers to a peptide as described herein.

Although the descriptions of pharmaceutical compositions provided hereinare principally directed to pharmaceutical compositions foradministration to humans, it will be understood by the skilled artisanthat such compositions are generally suitable for administration toanimals of all sorts. Modification of pharmaceutical compositions foradministration to various animals is well understood, and the ordinarilyskilled veterinary pharmacologist can design and/or perform suchmodification with merely ordinary, if any, experimentation.

Pharmaceutical compositions described herein may be prepared by anymethod known or hereafter developed in the art of pharmacology. Ingeneral, such preparatory methods include the step of bringing theactive ingredient into association with an excipient and/or one or moreother accessory ingredients, and then, if necessary and/or desirable,shaping and/or packaging the product into a desired single- ormulti-dose unit.

A pharmaceutical composition of the invention may be prepared, packaged,and/or sold in bulk, as a single unit dose, and/or as a plurality ofsingle unit doses. As used herein, a “unit dose” is discrete amount ofthe pharmaceutical composition comprising a predetermined amount of theactive ingredient. The amount of the active ingredient is generallyequal to the dosage of the active ingredient which would be administeredto a subject and/or a convenient fraction of such a dosage such as, forexample, one-half or one-third of such a dosage.

The relative amounts of the active ingredient, the pharmaceuticallyacceptable excipient, and/or any additional ingredients in apharmaceutical composition of the invention will vary, depending uponthe identity, size, and/or disorder of the subject treated and furtherdepending upon the route by which the composition is to be administered.By way of example, the composition may comprise between 0.1% and 100%(w/w) active ingredient.

As used herein, a pharmaceutically acceptable excipient includes any andall solvents, dispersion media, diluents, or other liquid vehicles,dispersion or suspension aids, surface active agents, isotonic agents,thickening or emulsifying agents, preservatives, solid binders,lubricants and the like, as suited to the particular dosage formdesired. Remington's The Science and Practice of Pharmacy, 21^(St)Edition, A. R. Gennaro, (Lippincott, Williams & Wilkins, Baltimore, Md.,2006) discloses various excipients used in formulating pharmaceuticalcompositions and known techniques for the preparation thereof. Exceptinsofar as any conventional carrier medium is incompatible with asubstance or its derivatives, such as by producing any undesirablebiological effect or otherwise interacting in a deleterious manner withany other component(s) of the pharmaceutical composition, its use iscontemplated to be within the scope of this invention.

In some embodiments, the pharmaceutically acceptable excipient is atleast 95%, 96%, 97%, 98%, 99%, or 100% pure. In some embodiments, theexcipient is approved for use in humans and for veterinary use. In someembodiments, the excipient is approved by the United States Food andDrug Administration. In some embodiments, the excipient ispharmaceutical grade. In some embodiments, the excipient meets thestandards of the United States Pharmacopoeia (USP), the EuropeanPharmacopoeia (EP), the British Pharmacopoeia, and/or the InternationalPharmacopoeia.

Pharmaceutically acceptable excipients used in the manufacture ofpharmaceutical compositions include, but are not limited to, inertdiluents, dispersing and/or granulating agents, surface active agentsand/or emulsifiers, disintegrating agents, binding agents,preservatives, buffering agents, lubricating agents, and/or oils. Suchexcipients may optionally be included in the inventive formulations.Excipients such as cocoa butter and suppository waxes, coloring agents,coating agents, sweetening, flavoring, and perfuming agents can bepresent in the composition, according to the judgment of the Formulator.

Exemplary diluents include, but are not limited to, calcium carbonate,sodium carbonate, calcium phosphate, dicalcium phosphate, calciumsulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose,cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol,inositol, sodium chloride, dry starch, cornstarch, powdered sugar, andcombinations thereof

Exemplary granulating and/or dispersing agents include, but are notlimited to, potato starch, corn starch, tapioca starch, sodium starchglycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite,cellulose and wood products, natural sponge, cation— exchange resins,calcium carbonate, silicates, sodium carbonate, cross—linked poly(vinyl—pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starchglycolate), carboxymethyl cellulose, cross—linked sodium carboxymethylcellulose (croscarmellose), methylcellulose, pregelatinized starch(starch 1500), microcrystalline starch, water insoluble starch, calciumcarboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodiumlauryl sulfate, quaternary ammonium compounds, and combinations thereof

Exemplary surface active agents and/or emulsifiers include, but are notlimited to, natural emulsifiers (e.g. acacia, agar, alginic acid, sodiumalginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin,egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidalclays (e.g. bentonite [aluminum silicate] and Veegum [magnesium aluminumsilicate]), long chain amino acid derivatives, high molecular weightalcohols (e.g. stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetinmonostearate, ethylene glycol distearate, glyceryl monostearate, andpropylene glycol monostearate, polyvinyl alcohol), carbomers (e.g.carboxy polymethylene, polyacrylic acid, acrylic acid polymer, andcarboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g.carboxymethylcellulose sodium, powdered cellulose, hydroxymethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose,methylcellulose), sorbitan fatty acid esters (e.g. polyoxyethylenesorbitan monolaurate [Tween 20], polyoxyethylene sorbitan [Tween 60],polyoxyethylene sorbitan monooleate [Tween 80], sorbitan monopalmitate[Span 40], sorbitan monostearate [Span 60], sorbitan tristearate [Span65], glyceryl monooleate, sorbitan monooleate [Span 80]),polyoxyethylene esters (e.g. polyoxyethylene monostearate [Myrj 45],polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil,polyoxymethylene stearate, and Solutol), sucrose fatty acid esters,polyethylene glycol fatty acid esters (e.g. Cremophor), polyoxyethyleneethers, (e.g. polyoxyethylene lauryl ether [Brij 30]),poly(vinyl—pyrrolidone), diethylene glycol monolaurate, triethanolamineoleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyllaurate, sodium lauryl sulfate, Pluronic F 68, Poloxamer 188,cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride,docusate sodium, and/or combinations thereof

Exemplary binding agents include, but are not limited to, starch (e.g.cornstarch and starch paste); gelatin; sugars (e.g. sucrose, glucose,dextrose, dextrin, molasses, lactose, lactitol, mannitol,); natural andsynthetic gums (e.g. acacia, sodium alginate, extract of Irish moss,panwar gum, ghatti gum, mucilage of isapol husks,carboxymethylcellulose, methylcellulose, ethylcellulose,hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropylmethylcellulose, microcrystalline cellulose, cellulose acetate,poly(vinyl—pyrrolidone), magnesium aluminum silicate (Veegum), and larcharabogalactan); alginates; polyethylene oxide; polyethylene glycol;inorganic calcium salts; silicic acid; polymethacrylates; waxes; water;alcohol; and combinations thereof

Exemplary preservatives may include antioxidants, chelating agents,antimicrobial preservatives, antifungal preservatives, alcoholpreservatives, acidic preservatives, and other preservatives. Exemplaryantioxidants include, but are not limited to, alpha tocopherol, ascorbicacid, acorbyl palmitate, butylated hydroxyanisole, butylatedhydroxytoluene, monothioglycerol, potassium metabisulfite, propionicacid, propyl gallate, sodium ascorbate, sodium bisulfite, sodiummetabisulfite, and sodium sulfite. Exemplary chelating agents includeethylenediaminetetraacetic acid (EDTA), citric acid monohydrate,disodium edetate, dipotassium edetate, edetic acid, fumaric acid, malicacid, phosphoric acid, sodium edetate, tartaric acid, and trisodiumedetate. Exemplary antimicrobial preservatives include, but are notlimited to, benzalkonium chloride, benzethonium chloride, benzylalcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine,chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol,glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethylalcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.Exemplary antifungal preservatives include, but are not limited to,butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoicacid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodiumbenzoate, sodium propionate, and sorbic acid. Exemplary alcoholpreservatives include, but are not limited to, ethanol, polyethyleneglycol, phenol, phenolic compounds, bisphenol, chlorobutanol,hydroxybenzoate, and phenylethyl alcohol. Exemplary acidic preservativesinclude, but are not limited to, vitamin A, vitamin C, vitamin E,beta—carotene, citric acid, acetic acid, dehydroacetic acid, ascorbicacid, sorbic acid, and phytic acid. Other preservatives include, but arenot limited to, tocopherol, tocopherol acetate, deteroxime mesylate,cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened(BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ethersulfate (SLES), sodium bisulfite, sodium metabisulfite, potassiumsulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben,Germall 115, Germaben II, Neolone, Kathon, and Euxyl. In certainembodiments, the preservative is an anti-oxidant. In other embodiments,the preservative is a chelating agent.

Exemplary buffering agents include, but are not limited to, citratebuffer solutions, acetate buffer solutions, phosphate buffer solutions,ammonium chloride, calcium carbonate, calcium chloride, calcium citrate,calcium glubionate, calcium gluceptate, calcium gluconate, D—gluconicacid, calcium glycerophosphate, calcium lactate, propanoic acid, calciumlevulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid,tribasic calcium phosphate, calcium hydroxide phosphate, potassiumacetate, potassium chloride, potassium gluconate, potassium mixtures,dibasic potassium phosphate, monobasic potassium phosphate, potassiumphosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride,sodium citrate, sodium lactate, dibasic sodium phosphate, monobasicsodium phosphate, sodium phosphate mixtures, tromethamine, magnesiumhydroxide, aluminum hydroxide, alginic acid, pyrogen—free water,isotonic saline, Ringer's solution, ethyl alcohol, ., and combinationsthereof

Exemplary lubricating agents include, but are not limited to, magnesiumstearate, calcium stearate, stearic acid, silica, talc, malt, glycerylbehanate, hydrogenated vegetable oils, polyethylene glycol, sodiumbenzoate, sodium acetate, sodium chloride, leucine, magnesium laurylsulfate, sodium lauryl sulfate, ., and combinations thereof

Exemplary oils include, but are not limited to, almond, apricot kernel,avocado, babassu, bergamot, black current seed, borage, cade, camomile,canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, codliver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose,fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop,isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon,litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink,nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel,peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary,safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, sheabutter, silicone, soybean, sunflower, tea tree, thistle, tsubaki,vetiver, walnut, and wheat germ oils. Exemplary oils include, but arenot limited to, butyl stearate, caprylic triglyceride, caprictriglyceride, cyclomethicone, diethyl sebacate, dimethicone 360,isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol,silicone oil, and combinations thereof

General considerations in the formulation and/or manufacture ofpharmaceutical agents may be found, for example, in Remington: TheScience and Practice of Pharmacy 21^(st) ed., Lippincott Williams &Wilkins, 2005.

Inventive peptides provided herein are typically formulated in dosageunit form for ease of administration and uniformity of dosage. It willbe understood, however, that the total daily usage of the compositionsof the present invention will be decided by the attending physicianwithin the scope of sound medical judgment. The specific therapeuticallyeffective dose level for any particular subject will depend upon avariety of factors including the disease, disorder, or disorder beingtreated and the severity of the disorder; the activity of the specificactive ingredient employed; the specific composition employed; the age,body weight, general health, sex and diet of the subject; the time ofadministration, route of administration, and rate of excretion of thespecific active ingredient employed; the duration of the treatment;drugs used in combination or coincidental with the specific activeingredient employed; and like factors well known in the medical arts.

The peptides provided herein or pharmaceutical composition thereof, maybe administered by any route. In some embodiments, the peptide orpharmaceutical composition thereof, are administered by a variety ofroutes, including oral, intravenous, intramuscular, intra—arterial,intramedullary, intrathecal, subcutaneous, intraventricular,transdermal, intradermal, rectal, intravaginal, intraperitoneal, topical(as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal,enteral, sublingual; by intratracheal instillation, bronchialinstillation, and/or inhalation; and/or as an oral spray, nasal spray,and/or aerosol. Specifically contemplated routes are systemicintravenous injection, regional administration via blood and/or lymphsupply, and/or direct administration to an affected site. In general themost appropriate route of administration will depend upon a variety offactors including the nature of the agent (e.g., its stability in theenvironment of the gastrointestinal tract), and the disorder of thesubject (e.g., whether the subject is able to tolerate oraladministration). At present the oral and/or nasal spray and/or aerosolroute is most commonly used to deliver therapeutic agents directly tothe lungs and/or respiratory system. However, the invention encompassesthe delivery of the inventive pharmaceutical composition by anyappropriate route taking into consideration likely advances in thesciences of drug delivery.

In certain embodiments, the peptides or pharmaceutical compositionthereof, may be administered at dosage levels sufficient to deliver fromabout 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50mg/kg, from about 0.1 mg/kg to about 40 mg/kg, from about 0.5 mg/kg toabout 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1mg/kg to about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg, ofsubject body weight per day, one or more times a day, to obtain thedesired therapeutic effect. The desired dosage may be delivered threetimes a day, two times a day, once a day, every other day, every thirdday, every week, every two weeks, every three weeks, or every fourweeks. In certain embodiments, the desired dosage may be delivered usingmultiple administrations (e.g., two, three, four, five, six, seven,eight, nine, ten, eleven, twelve, thirteen, fourteen, or moreadministrations).

It will be appreciated that dose ranges as described herein provideguidance for the administration of provided pharmaceutical compositionsto an adult. The amount to be administered to, for example, a child oran adolescent can be determined by a medical practitioner or personskilled in the art and can be lower or the same as that administered toan adult. The exact amount of an inventive peptide required to achievean effective amount will vary from subject to subject, depending, forexample, on species, age, and general disorder of a subject, severity ofthe side effects or disorder, identity of the particular compound(s),mode of administration, and the like.

In some embodiments, the present invention encompasses “therapeuticcocktails” comprising inventive peptides. In some embodiments, theinventive peptide comprises a single species which can bind to multipletargets. In some embodiments, different inventive peptides comprisedifferent targeting moiety species, and all of the different targetingmoiety species can bind to the same target. In some embodiments,different inventive peptides comprise different targeting moietyspecies, and all of the different targeting moiety species can bind todifferent targets. In some embodiments, such different targets may beassociated with the same cell type. In some embodiments, such differenttargets may be associated with different cell types.

It will be appreciated that inventive peptides and pharmaceuticalcompositions of the present invention can be employed in combinationtherapies. The particular combination of therapies (therapeutics orprocedures) to employ in a combination regimen will take into accountcompatibility of the desired therapeutics and/or procedures and thedesired therapeutic effect to be achieved. It will be appreciated thatthe therapies employed may achieve a desired effect for the same purpose(for example, an inventive conjugate useful for detecting tumors may beadministered concurrently with another agent useful for detectingtumors), or they may achieve different effects (e.g., control of anyadverse effects).

Pharmaceutical compositions of the present invention may be administeredeither alone or in combination with one or more therapeutically activeagents. By “in combination with,” it is not intended to imply that theagents must be administered at the same time and/or formulated fordelivery together, although these methods of delivery are within thescope of the invention. The compositions can be administeredconcurrently with, prior to, or subsequent to, one or more other desiredtherapeutics or medical procedures. In general, each agent will beadministered at a dose and/or on a time schedule determined for thatagent. Additionally, the invention encompasses the delivery of theinventive pharmaceutical compositions in combination with agents thatmay improve their bioavailability, reduce and/or modify theirmetabolism, inhibit their excretion, and/or modify their distributionwithin the body. It will further be appreciated that therapeuticallyactive agent and the inventive peptides utilized in this combination maybe administered together in a single composition or administeredseparately in different compositions.

The particular combination employed in a combination regimen will takeinto account compatibility of the therapeutically active agent and/orprocedures with the inventive peptide and/or the desired therapeuticeffect to be achieved. It will be appreciated that the combinationemployed may achieve a desired effect for the same disorder (forexample, an inventive peptide may be administered concurrently withanother therapeutically active agent used to treat the same disorder),and/or they may achieve different effects (e.g., control of any adverseeffects).

As used herein, a “therapeutically active agent” refers to any substanceused as a medicine for treatment, prevention, delay, reduction oramelioration of a disorder, and refers to a substance that is useful fortherapy, including prophylactic and therapeutic treatment. Atherapeutically active agent also includes a compound that increases theeffect or effectiveness of another compound, for example, by enhancingpotency or reducing adverse effects of the inventive peptides.

In certain embodiments, a therapeutically active agent is an anti-canceragent, antibiotic, anti-viral agent, anti-HIV agent, anti-parasiteagent, anti-protozoal agent, anesthetic, anticoagulant, inhibitor of anenzyme, steroidal agent, steroidal or non-steroidal anti-inflammatoryagent, antihistamine, immunosuppressant agent, anti-neoplastic agent,antigen, vaccine, antibody, decongestant, sedative, opioid, analgesic,anti-pyretic, birth control agent, hormone, prostaglandin,progestational agent, anti-glaucoma agent, ophthalmic agent,anti-cholinergic, analgesic, anti-depressant, anti-psychotic,neurotoxin, hypnotic, tranquilizer, anti-convulsant, muscle relaxant,anti-Parkinson agent, anti-spasmodic, muscle contractant, channelblocker, miotic agent, anti-secretory agent, anti-thrombotic agent,anticoagulant, anti-cholinergic, β-adrenergic blocking agent, diuretic,cardiovascular active agent, vasoactive agent, vasodilating agent,anti-hypertensive agent, angiogenic agent, modulators ofcell-extracellular matrix interactions (e.g. cell growth inhibitors andanti-adhesion molecules), or inhibitors/intercalators of DNA, RNA,protein-protein interactions, protein-receptor interactions.

In some embodiments, inventive pharmaceutical compositions may beadministered in combination with any therapeutically active agent orprocedure (e.g., surgery, radiation therapy) that is useful to treat,alleviate, ameliorate, relieve, delay onset of, inhibit progression of,reduce severity of, and/or reduce incidence of one or more symptoms orfeatures of cancer.

Kits

Provided herein are a variety of kits comprising one or more of thepeptides of the invention. For example, the invention provides a kitcomprising an inventive peptide and instructions for use. A kit maycomprise multiple different peptides. A kit may comprise any of a numberof additional components or reagents in any combination. All of thevarious combinations are not set forth explicitly but each combinationis included in the scope of the invention.

According to certain embodiments of the invention, a kit may include,for example, (i) one or more inventive peptides and, optionally, one ormore particular therapeutically active agents to be delivered; (ii)instructions for administration to a subject in need thereof.

Kits typically include instructions which may, for example, compriseprotocols and/or describe disorders for production of inventivepeptides, administration of inventive peptides to a subject in needthereof, design of novel inventive peptide. Kits will generally includeone or more vessels or containers so that some or all of the individualcomponents and reagents may be separately housed. Kits may also includea means for enclosing individual containers in relatively closeconfinement for commercial sale, e.g., a plastic box, in whichinstructions, packaging materials such as styrofoam, may be enclosed. Anidentifier, e.g., a bar code, radio frequency identification (ID) tag,may be present in or on the kit or in or one or more of the vessels orcontainers included in the kit. An identifier can be used, e.g., touniquely identify the kit for purposes of quality control, inventorycontrol, tracking, movement between workstations.

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. It should beunderstood that these examples are for illustrative purposes only andare not to be construed as limiting this invention in any manner.

EXAMPLES

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. It should beunderstood that these examples are for illustrative purposes only andare not to be construed as limiting this invention in any manner.

Experimental Methods

General Methods. Oligonucleotide primers were ordered from Eurofins MWGOperon or Integrated DNA Technologies. Trimerphosphoroamidite-containing primers were ordered from the Yale KeckOligo facility, synthesized with trimer phosphoroamitide building blocks(Glen Research). PCR was performed with LongAmp Taq polymerase (NewEngland Biolabs) and purified with a PCR cleanup kit (Qiagen). Plasmidswere propagated in E. coli with standard methods and purified using aminiprep kit (Qiagen). Absorbance measurements were performed with aNanoDrop 2000C spectrophotometer (Thermo Scientific). HPLC was performedwith an Agilent 1200 series instrument equipped with a Supelco 250×10 mmC18 column. LC/MS was performed with an Agilent 1260 series instrumentequipped with an Agilent 150×2.1 mm C18 column, connected to an Agilent1100 series quadrupole MSD. Gel filtration and desalting were performedon an Akta FPLC (Amersham/GE Healthcare).

Peptide Synthesis. Peptides were synthesized on the solid phase bystandard Fluorenylmethyloxycarbonyl chloride (Fmoc) methods, typicallyon a 30 μmol scale using Rink amide resin. The N-terminal Fmocprotecting group of the resin-bound peptide was removed by two 10minutes treatments of 25% piperidine in N-Methyl-2-pyrrolidone (NMP),followed by four washes of NMP. Fmoc-protected amino acid (6equivalents, at 0.19 M final concentration) were pre-mixed with PyClock(5.7 equivalents) and N,N-Diisopropylethylamine (DIEA, 12 equivalents),then bubbled with the resin under nitrogen for 1 hour. For couplingsexpected to be difficult (e.g. following a,a-disubstituted amino acids,β-branched amino acids, and proline) two sequential 1-hour couplingreactions were done. After coupling, the resin was washed four times inNMP and de-protected as before. Olefin methathesis was carried out withtwo 2-hour treatments of 10 mM Grubbs I catalyst in 1,2-dichloroethane(DCE). FITC was added to the peptide N-terminus by bubbling resinovernight in 30 mg/ml FITC with 10% v/v DIEA in NMP. Following thesynthesis, peptides were deprotected and cleaved in 95% trifluoroaceticacid (TFA), 2.5% triisopropylsilane (TIS), and 2.5% H₂O, then purifiedby high-performance liquid chromatography (HPLC) using a 10-100%gradient of acetonitrile in H₂O with 0.1% TFA. Collected fractions weredried by speedvac and lyophilization.

Circular Dichroism Spectroscopy. CD measurements were carried out on aJasco J-710 spectrophotometer equipped with a PTC-348W temperaturecontroller. Samples (˜190 μl) were placed in a 1 mm quartz cuvette(sealed with parafilm) at 20-80 μM in 50 mM sodium phosphate pH 8 unlessotherwise noted. For spectra, the CD was scanned from 260 nm to 190 nmat a scanning speed of 20 nm/min in 0.1 nm increments at 25° C. Formelting curves, the temperature was increased from 10 to 90° C. at arate 2° C./min while recording the CD at 222 nm. Raw curves weresmoothened using a Savitzky-Golay filter.

Matrix-assisted laser desorption/ionization. MALDI was performed on aWaters MALDI Micro MX. 200 pmol of protein was raised to 20 ul in watercontaining 0.1% TFA, then bound to a ZipTip μC18 tip, washed with water+0.1% TFA, then eluted with 50% MeCN+0.1% TFA. Samples were added to ametal MALDI plate that had been pre-spotted with a saturated solution ofsinapinic acid in 40% MeCN +0.1% TFA, then air-dried before analysis.

Library Transformation into Yeast. Yeast display protocols weregenerally carried out as described by Wittrup and colleagues. ^(1,2)Yeast density was quantified by absorbance (1 AU₆₀₀=10⁷ cells/ml), andcells were pelleted at 15,000×g for ˜45 seconds (in 1.5 ml eppendorftube) or at 2,500×g for 3 minutes (for larger volumes). LinearizedpCTCON2 (1 μg) was mixed with PCR insert (4 μg) and precipitated byraising to 100 μl in water, adding 2 μl of PelletPaint (Novagen)followed by 10 ul of 4 M NH₄Ac, mixing, then adding 200 μl of ethanoland incubating for 5 minutes. The DNA was pelleted, washed with 200 μlof 70% ethanol, then washed with 100% ethanol and air-dried. The DNA wasresuspended in 2μl of water and stored at 4° C. until transformation. S.cerevisiae strain EBY100 (obtained from K. Dane Wittrup, MassachusettsInstitute of Technology) was grown in YPD media at 30° C., shaking at225 rpm. Cells were passaged twice prior to transformation to ensure ahealthy culture. The day of the transformation, cells were diluted to anOD₆₀₀ of 0.1 in 110 ml of YPD media and grown until OD₆₀₀=1.4, at whichpoint 1 ml of Tris-DTT buffer (2.5 M DTT in 1 M Tris pH 8) was added.After 15 additional minutes of shaking, the cells were pelleted,resuspended in 50 ml of 10 mM Tris, 270 mM sucrose, 1 mM MgCl₂, pH 7.5,pelleted again, and washed with a further 25 ml of the same buffer. Thecells were resuspended to a final volume of ˜600 ul with buffer, thenmixed with precipitated library DNA (1 μg vector/4 μg insert per 50 ulcells) and incubated for 10 minutes before electroporating at 0.54 kV,25 μF in a GenePulser II electroporator (Bio-Rad). Cells wereimmediately rescued into 30 ml of pre-warmed 30° C. YPD, transferred toa 30° C. shaker for 60 minutes, then pelleted and resuspended in SDCAAmedia supplemented with ampicillin and kanamycin. Serial dilutions wereplated onto SDCAA plates to determine the library transformationefficiency. For generation of library templates using error-prone PCR,the method of Zaccolo et al.³ utilizing dPTP and 8-oxo-dGTP was used asdescribed in Chao et al.¹

Screening Yeast Libraries by MACS. Yeast libraries were grown in SDCAAmedia, then passaged into SGCAA media 20-24 hours prior to sorting.Yeast (up to 5 * 10⁹ cells) were pelleted, washed with MACS buffer (15mM sodium phosphate pH 7.4, 150 mM NaCl, 5 mM KCl, 0.5% w/v BSA), thenincubated with biotinylated Ras for 45-60 minutes at a density of 10⁹cells/ml at room temperature before pelleting, washing with buffer, andresuspending in 1 ml of buffer. Anti-biotin microbeads (50 ul, Miltenyi)were added and the cells were rotated at 4° C. for 30 minutes, thenseparated on an AutoMACS instrument (Miltenyi) using the Possel_sprogram. Eluted cells were resuspended in SDCAA and a 1/100 dilution wasplated on SDCAA to estimate the number of retained cells.

Screening Yeast Libraries by FACS. Yeast libraries were grown in SDCAAmedia, then passaged into SGCAA media 20-24 hours prior to sorting.Yeast cells were pelleted, washed with FACS buffer (15 mM sodiumphosphate pH 7.4, 150 mM NaCl, 5 mM KCl, 0.1% w/v BSA), then incubatedwith biotinylated Ras for 45-60 minutes at room temperature beforepelleting, washing with buffer, and resuspending in 100 ul of buffer per10⁷ cells. Ras incubation was done at a density of 10⁷ cells/ml unlessthe concentration of [Ras] fell below 100 nM; in this case, the bindingvolume was chosen such that there were at least 500,000 molecules of Rasper yeast cell (per the guidelines of Chao et al'). Secondary reagentswere then added (Anti-HA Alexa488 at a 1:200 dilution, and either SA-PE,SA-APC, or NA-PE at a 1:100 dilution) and incubated for 10 minutes at 4°C. in the dark before pelleting, washing, and re-pelleting. Immediatelyprior to sorting, the cells were resuspended in FACS buffer to anapproximate density of 2 * 10⁷ cells/ml.

Expression and Purification of Ras Proteins. Ras proteins wererecombinantly expressed in E. coli BL21 Rosetta I pLysS cells withC-terminal His₆ (SEQ ID NO:55) and yBBr tags. The identity of theplasmid backbone is not known (parent KRas vector was originallyobtained from Johannes Yeh) but is likely pET-derived, with ampicillinresistance. The cells were grown to OD₆₀₀=0.7, induced with 0.3 mM IPTGfor 5 hours at 30° C., then harvested and resuspended in 50 mM Tris pH7.5 at 4° C., 300 mM NaCl, 10 mM imidazole, 5 mM MgCl₂ prior tosnap-freezing in liquid nitrogen. For purification, the pellet wasthawed, raised to 40 ml in the same buffer, and mixed with a RocheComplete EDTA-free protease inhibitor tablet. The cells were lysed witha tip sonicator (VirSonic, 6 cycles of 10 s on, 15 s off at 6.5 powerlevel), then pelleted at 30,000×g for 30 minutes and filtered through a1.2 uM Supor membrane (Pall Corporation). The clarified lysate was addedto 2 ml of HisPur Cobalt resin (Thermo Pierce) that had beenequilibrated with the lysis buffer, and drained by gravity. The columnwas washed with 20 ml of buffer, then protein was eluted with —5 ml ofbuffer containing 150 mM imidazole. Immediately following elution fromthe column, DTT was added for a final concentration of ˜1 mM and a smallportion of protease inhibitor (reserved from the lysis step) was added.The protein was concentrated in a Centriprep YM-10 (Millipore) to 2 mland purified by gel filtration on a Superdex 75 10/300 column (GEHealthcare) into 50 mM Tris pH 7.4, 100 mM NaCl, 5 mM MgCl₂, 1 mM DTT.For long-term storage, proteins were concentrated to >100 μM, mixed withglycerol to 10%, and snap-frozen in liquid nitrogen and stored at −80°C.

Rap1a, RalA, and Rab25 were expressed and purified following the sameprotocol. Rapla and RalA were cloned into identical (His6 (SEQ IDNO:55)/yBBr tagged) vectors as for the Ras proteins; His₆-tagged (SEQ IDNO:55) Rab25 was expressed from a pET vector.

Nucleotide Exchange with Calf Intestinal Alkaline Phosphatase. Forenzymatic nucleotide exchange, the Ras protein was buffer exchanged bygel filtration on a Superdex 75 10/300 column into 32 mM Tris pH 8, 200mM (NH₄)₂SO₄, 1 mM DTT, 0.5 mM NaN3, 1μM ZnCl₂. The protein wasconcentrated to >100 μM, then mixed with GppNHp or GppCp to 0.5-1.0 mM,followed by 10-20 units of calf intestinal alkaline phosphatase (NewEngland Biolabs). The protein was incubated at room temperature for 30minutes, then MgCl₂ was added to 5 mM and the protein was gel filteredas before into 50 mM Tris pH 7.4, 100 mM NaCl, 5 mM MgCl₂, 1 mM DTT. Forsubsequent exchange to GTP or GDP, Ras protein loaded with GppCp wasincubated with a 50-100 fold excess of desired nucleotide in thepresence of 10 mM EDTA for 30 minutes at room temperature before addingMgCl₂ to 20 mM and removing excess nucleotide by gel filtration asusual.

Quantification of nucleotide loading by HPLC. Ras proteins (˜2 nmol)were raised to 150 ul with ultrapure water, then mixed with 150 ul of100 mM potassium phosphate pH 6.5, 10 mM tetrabutylammonium bromide.Samples were analyzed by reverse-phase HPLC (Supelco semi-prep C18column) using a 20 minute isocratic run in 100 mM potassium phosphate pH6.5, 10 mM tetrabutylammonium bromide, 7.5% acetonitrile. Elution timesfor GDP, GTP, and GppNHp were determined with the pure nucleotide (SigmaAlrich).

Purification of B-Raf RBD. The Raf RBD was recombinantly expressed in E.coli BL21 Rosetta I pLysS cells with an N-terminal glutathioneS-transferase (GST) tag. The gene for the RBD was subcloned into apGEX-₅X plasmid (GE Healthcare) by Johannes Yeh. The cells were grown toOD₆₀₀=0.7, induced with 0.3 mM IPTG for 5 hours at 30° C., thenharvested and resuspended in lysis buffer (PBS +1 mM DTT and 0.5 mMEDTA) prior to snap-freezing in liquid nitrogen. For purification, thepellet was thawed, raised to 40 ml in the same buffer, and mixed with aRoche Complete EDTA-free protease inhibitor tablet. The cells were lysedwith a tip sonicator (VirSonic, 6 cycles of 10 s on, 15 s off at 6.5power level), then pelleted at 30,000×g for 30 minutes and filteredthrough a 1.2 uM Supor membrane (Pall Corporation). The clarified lysatewas added to 2 ml of immobilized glutathione resin (Thermo Pierce) thathad been equilibrated with the lysis buffer, and drained by gravity. Thecolumn was washed with 20 ml of buffer, then protein was eluted with 50mM Tris pH 8.0, 10 mM reduced glutathione, 1 mM DTT, 0.5 mM EDTA. Thesample was concentrated in a Centriprep YM-10 (Millipore) to 2 ml andpurified by gel filtration on a Superdex 200 10/300 column (GEHealthcare) into 50 mM Tris pH 7.4, 100 mM NaCl, 5 mM MgCl₂, 1 mM DTT.For long-term storage, proteins were concentrated to >100 μM, mixed withglycerol to 10%, and snap-frozen in liquid nitrogen and stored at −80°C.

Purification of Sfp phosphopantetheinyl transferase. Sfp wasrecombinantly expressed in E. coli BL21 cells from a pET29-Sfp vectorobtained from Christopher Walsh (Harvard Medical School). The cells weregrown to OD₆₀₀=0.7, induced with 1 mM IPTG for 6 hours at 25° C.,harvested and resuspended in 50 mM sodium phosphate pH 7.5, 300 mM NaCl,10 mM imidazole prior to snap-freezing in liquid nitrogen. The proteinwas purified by Cobalt affinity chromatography as described above forthe Ras proteins. The purified protein was gel filtered on a Superdex 7510/300 column (GE Healthcare) into 10 mM Tris pH 7.5, 1 mM EDTA, 10%glycerol. Fractions eluting with the peak at ˜15 ml were pooled, splitinto aliquots, snap-frozen in liquid nitrogen, and stored at −80° C.

Synthesis of Biotin-CoA (LK04). Coenzyme A (Sigma-Aldrich, 10 mM inDulbecco's phosphate-buffered saline) was mixed with one equivalent ofBiotin-Peg₂-Maleimide (Thermo Pierce, 20 mM in 50 mM Tris, pH 7)followed by 0.2 equivalents of TCEP (Sigma-Aldrich, 0.5 M in water). Thereaction was incubated at room temperature for 2 hours, then purified byHPLC using a 20 minute 0-40% MeCN gradient in water with 0.1% TFA.

Synthesis of Alexa647-CoA (LK06). Coenzyme A (Sigma-Aldrich, 10 mM inDulbecco's phosphate-buffered saline) was diluted to 5 mM in 50 mM TrispH 7, then TCEP was added to 7.5 mM (3 ul of a 500 mM stock). After 5minutes, 1 mg of Alexa647-C2-maleimide (Life Technologies) was dissolvedin 34 ul of DMSO and added to the reaction, and incubated in the dark atroom temperature for 45 minutes before diluting the reaction with 500 ulof milliQ and purifying by HPLC using a 20 minute 0-60% MeCN gradient inwater with 0.1% TFA.

Protein labeling by Sfp phosphopantetheinyl transferase. Purified Raswas gel filtered on a Superdex 75 10/300 column into 64 mM Tris pH 7.5,5 mM MgCl₂, 1 mM DTT. Ras (50-150 μM) was mixed with 1.0-1.3 equivalentsof CoA linker (LK04 or LK06), followed by Sfp to 3-5 μM. The reactionwas incubated at room temperature for 1 hour, then gel filtered asbefore into 50 mM Tris pH 7.4, 100 mM NaCl, 5 mM MgCl₂, 1 mM DTT.

Recombinant production of 225 peptides. pET30a (Novagen) was digestedwith NcoI-HF and XhoI (New England Biolabs) and ligated with a PCRfragment containing the peptide sequence with 5′ NcoI and 3′ XhoI sites.To shuttle the ORF into an ampicillin-resistant plasmid (for expressionstrain compatibility reasons), this plasmid was digested with XbaI andXhoI (New England Biolabs) and the insert subcloned into a pET19b vector(Novagen). The resulting plasmids were transformed into BL21 cellscontaining the pG-KJE8 plasmid (Clontech), which carries the dnaK, dnaJ,grpE, GroEL, and GroES chaperones under control of anarabinose-inducible promoter. Cells were grown in LB media at 37° C. toan OD₆₀₀ of ˜0.7, then induced with 500 μM of IPTG and 200 mg ofarabinose for 5 hours at 30° C. The cells were pelleted at 5,000×g for15 minutes, resuspended in 50 mM sodium phosphate pH 7.5, 1000 mM NaCl,10 mM imidazole, and snap-frozen. All subsequent steps were performed at4° C. The pellet was thawed and mixed with EDTA-free protease inhibitor(Roche), lysed with a tip sonicator (VirSonic, 6 cycles of 10 s on, 15 soff at 6.5 power level), then pelleted at 30,000×g for 30 minutes andfiltered through a 1.2 μM filter. The clarified lysate was rocked with 2ml of cobalt resin (Thermo Pierce) for 30 minutes, then transferred to acolumn and drained by gravity. The resin was washed with ˜20 ml of lysisbuffer, then the fusion protein was eluted with lysis buffer containing350 mM imidazole. DTT and EDTA were added to concentrations of 1 mM and0.5 mM, respectively, along with protease inhibitor (Roche). The elutedprotein was concentrated to 2 ml, buffer exchanged into 50 mM Tris pH 8,250 mM NaCl, 1 mM DTT, 0.5 mM EDTA using two tandem 5 ml HiTrapDesalting columns (GE Healthcare), then cleaved with TEV proteaseovernight at room temperature. The cleavage reaction was passed over twotandem SepPak Classic C18 cartridges (Waters) to bind the peptide, thecartridges were washed with water +0.1% TFA, and then the peptide waseluted with 75% MeCN +0.1% TFA. After concentrating by speedvac, thepeptide was purified by HPLC using a 10-100% gradient of acetonitrile inH₂O with 0.1% TFA. Collected fractions were dried by speedvac andlyophilization.

Labeling of peptides with FITC. HPLC-purified peptides were diluted to250-500 μM in DMSO, then 2 equivalents of TCEP were added from a 5 mMTCEP stock in 50 mM Tris pH 7. After 5 minutes of incubation at rt, 2equivalents of N-(5-Fluoresceinyl)maleimide was added from a 2.5 mMstock in DMSO, and the reaction was incubated at rt for 30 minutes inthe dark. The sample was quenched by adding 50% MeCN +0.1% TFA, thenpurified by HPLC as for the unlabeled peptides.

Labeling of peptides with biotin. HPLC-purified peptides were diluted to250-500 μM in DMSO, then 2 equivalents of TCEP were added from a 50 mMTCEP stock in 50 mM Tris pH 7. After 5 minutes of incubation at rt, 2equivalents of Biotin-PEG₂-maleimide (Thermo Pierce) was added from a 20mM stock in 50 mM Tris pH 7, and the reaction was incubated at rt for 30minutes in the dark. The sample was quenched by adding 50% MeCN +0.1%TFA, then purified by HPLC as for the unlabeled peptides.

Fluorescence polarization. FITC-labeled peptides were diluted to 30 nMin 50 mM Tris pH 7.4, 100 mM NaCl, 5 mM MgCl₂, 1 mM DTT, then added to40 ul of 2× protein stock (in the same buffer) dispensed into a 384-wellblack microplate (Corning). The plate was rested for 45 minutes at roomtemperature, then fluorescence anisotropy was recorded on a SpectraMaxM5 (Molecular Devices) with excitation at 485 nm, emission at 525 nm,cutoff at 515 nm, PMT high, 100 reads, slow carriage speed, and a 500 mssettling time. Each concentration point was prepared in triplicate, andeach well was read twice (and averaged). Data were plotted using Prism(Graphpad) and fit to a one-site specific binding model with hillcoefficient.

Synthesis of mant nucleotides. Syntheses of mGppNHp and mGDP wereperformed as described by Hiratsuka.⁴ 20 umol of Guanosine5′-[β,γ-imido]triphosphate trisodium salt hydrate (GppNHp) or Guanodinediphosphate (GDP) (Sigma) was dissolved in 1000 ul of ultrapure water ina round-bottomed flask, and the pH was adjusted to ˜9.5 with 1 M NaOH.The solution was heated to 38° C. in a water bath, and N-Methylisatoicanhydride (65 umol, 3.25 equiv, Aldrich, crushed to a fine powder) wasadded in four portions over 1 hour while stirring and maintaining the pHat 9-10 with 1 M NaOH. After 3 hours, 1 M HCl was added to lower the pHto ˜7 and terminate the reaction, and the tube was incubated on ice toprecipitate excess N-Methylisatoic anhydride, then centrifuged at maxspeed for 5 minutes. The supernatant was removed, then the crudeproducts were purified by HPLC using a 0-60% gradient of acetonitrile inH₂O with 0.1% TFA. Collected fractions were dried by speedvac andlyophilization, and quantified by absorbance (ε₂₅₂=21500 at pH 7). Thesenucleotides were loaded onto Ras proteins using alkaline phosphatase asdescribed above for their unlabeled counterparts.

A general scheme for the synthesis of mantGppNHp is provided below.GppNHp was dissolved in ultrapure water at 38° C. and the pH wasadjusted to ˜9.5 with NaOH, then N-Methylisatoic anhydride (3 equiv) wasadded portionwise while maintaining the pH between 9 and 10 withperiodic addition of NaOH. After 3 hours, the reaction was terminatedwith HCl and the product was precipitated on ice before purifying byHPLC.

Mant nucleotide dissociation experiments. To the wells of a black96-well plate (Corning) was added 100 ul of buffer (50 mM Tris pH 7.4,100 mM NaCl, 5 mM MgCl₂, 1 mM DTT) containing 2 μM Raf or peptide,followed by 50 ul of 2 μM mant-nucleotide loaded Ras protein. Afterincubating for 10 minutes in the dark at rt, 50 ul of a 2.6 mM stock ofunlabeled nucleotide was added for final concentrations of 500 nM Ras, 1μM Raf or peptide, and 0.65 mM unlabeled nucleotide. The wells weremixed using a multichannel pipette, then the mant fluorescence wastracked over the course of 2 hours with a SpectraMax M5 (MolecularDevices), recording six reads every 30 seconds (excitation 370 nm,emission 450 nm, cutoff 435 nm).

Surface Plasmon Resonance. Biotinylated KRas (GppNHp or GDP) was dilutedto 50 nM in Biacore running buffer (50 mM Tris pH 7.4, 100 mM NaCl, 5 mMMgCl_(2, 2) mM DTT +0.02% Triton X-₁₀₀, filtered and degassed, with 1 uMGppNHp for the GppNHp-containing protein samples) and immobilized on aStreptavidin CAPture chip with a Biacore X₁₀₀ SPR system (GE Healthcare)that had been primed three times with buffer and conditioned with 3×60 streatments of CAPture regeneration solution. I recorded single-cycleruns with 180 second binding and 900 second stabilization, with a bufferwash after each regeneration step that preceded an analysis step. Thecustom parameters were as follows: Capture 1: 300 s A 2 ul/min, 120 sstabilization; Capture 2: 45 s @ 5 ul/min, 180 s stabilization, Sample:30 ul/min, Regeneration: 120 s A 10 ul/min, 60 s stabilization. I beganwith one startup cycle and two blank cycles for background subtraction,then did sample injections at 1.23 nM, 3.7 nM, 11 nM, 33 nM, and 100 nMof 225-3 peptide that was prepared from a freshly dissolved andquantified sample of 225-3 in 5 mM NaOH. All samples were prepared incap-free Biacore tubes (GE Healthcare). Data were processed and analyzedby the instrument software, using a two-step binding model.

Pulldown assays in Capan-1 cell lysate. Capan-1 adenocarcinoma cellswere obtained from the American Type Culture Collection and cultured at37° C. (humidified atmosphere at 5% CO2) in Iscove's Modified Dulbecco'sMedium (IMDM) with 20% fetal bovine serum and 1× antibiotic/antimycotic(anti-anti, Gibco) using 75 cm² culture flasks (Falcon). Cells from twoflasks were grown to ˜90% confluency, trypsinized for 15 minutes at 37°C., pelleted, washed with cold PBS, then lysed by incubating for 10minutes in 50 mM HEPES pH 7.5, 100 mM NaCl, 10 mM MgCl₂, 1 mM EDTA, 5 mMDTT, 1% v/v Triton X-100, and 5× HALT Protease Inhibitor (Thermo). Thecells were pelleted at 16,000×g for 10 minutes in a tabletop centrifuge,then the supernatant was snap-frozen and stored at −80° C. The day ofthe pulldowns, the lysate was thawed and diluted 10-fold in lysis buffercontaining only 0.01% v/v Triton X-₁₀₀ (high detergent concentrationsinterfere with the Ras-peptide interaction). All subsequent steps wereperformed at 4° C. For peptide pulldowns, the lysate was pre-incubatedwith mock or with Raf RBD (3 μM) for 10 minutes before addingbiotinylated 225-3 (5 μM) and incubating for 45 minutes, followed by theaddition of 50 ul of Streptavidin MyOne Ti Dynabeads (Life Technologies)that had been blocked with Dulbecco's PBS containing 0.1 mg/ml of BSAfor 10 minutes at rt. The samples were rotated for 30 minutes, then thebeads were collected with a magnet and washed with 3×400 μl of lysisbuffer containing 0.1% v/v Triton X-₁₀₀. The samples were eluted fromthe beads by boiling in SDS loading buffer for 5 minutes, then pelletingat 16,000×g in a tabletop centrifuge. For Raf RBD pulldowns, the lysatewas pre-incubated with mock or with peptide (10 μM) for 10 minutesbefore adding GST-tagged Raf RBD (5 μM) and 50 ul of glutathione agarosebeads (Thermo) and rotating for 60 minutes. The supernatant was removedby spinning through a filter column (Thermo) and the beads were washedwith 3×400 μl of lysis buffer containing 0.1% v/v Triton X-100. Thesamples were eluted from the beads by soaking in SDS loading buffer for5 minutes, then pelleting at 16,000×g in a tabletop centrifuge andboiling for 5 minutes. Samples were run out on a 10% SDS-PAGE gel at 150V for 45 minutes, then transferred to an 0.45 μm nitrocellulose membrane(Whatman) in 15 mM Tris, 192 mM glycine, 20% methanol using a westernblotting chamber (Invitrogen) at 50 V for 45 minutes. The membrane wasblocked for 1 hour with 5% dry nonfat milk in tris-buffered saline with0.1% v/v Tween-20 (TBS/T), washed with TBS/T, then incubated overnightat 4° C. in 5% BSA in TBS/T with a 1:1000 dilution of Anti-Ras rabbitmAb (Cell Signaling, #3339). The next day, the membrane was washed withTBS/T, incubated for 1 hour at rt with Anti-rabbit HRP conjugate (CellSignaling), washed once more, then visualized with SuperSignal West Picochemiluminescent imaging reagents (Thermo) and BioMax Light film(Kodak/Carestream Health).

Nuclear Magnetic Resonance. To prepare ¹⁵N-labeled KRas or peptide,cells were grown in minimal media containing 1 g/l of ¹⁵NH₄Cl andexpressed as for unlabeled protein. KRas and 225-1 were purified asdescribed above, then buffer exchanged into NMR buffer (50 mM HEPES pH7.4, 50 mM NaCl, 2 mM MgCl_(2, 2) mM TCEP, 0.1 mM EDTA, 0.02% NaN₃). Rasand peptide were mixed at <50 uM to avoid aggregation, then concentratedto 100-200 uM, mixed with 1/19 volumes of D₂O (final concentration of5%), filtered through an 0.45 um membrane, then added to a Shigemi BMS-3NMR sample tube. NMR experiments were performed at 298K, using TROSY, ona 700 MHz Bruker (equipped with cryoprobe). Data were processed withNMRpipe and visualized using NMRview.

Reduction Tests. Peptides were dissolved in buffer and incubated with 0mM, 5 mM, or 50 mM DTT before analyzing by reverse-phase HPLC. Reducedpeptides elute earlier than oxidized peptides, as determined by LC/MSanalysis of the samples.

Complex formation, crystallization and data collection. K-Ras/RDAcomplexes were formed by mixing K-Ras with 1.2 fold molar excess of RDApeptide at 25 μM K-Ras concentration in 20 mM Tris pH 8.0, 50 mM NaCl, 5mM MgCl₂. After incubation at for 1 hour, the complex was purified bysize exclusion chromatography. Crystals of K-Ras in complex with RDA1and GMP-PNP were grown after mixing 0.5 μl of complex (9 mg/ml in 20 mMTris pH 8.0, 50 mM NaCl, 5 mM MgCl₂) and 0.5 ul of reservoir solutioncontaining 0.3 M calcium chloride and 23% (w/v) PEG 3350.K-Ras/RDA2/GMP-PNP complex was crystallized using 0.5 ul of complex(11.5 mg/ml) mixed with 1 ul of the reservoir solution containing0.1-0.2 M ammonium sulfate, 20-22% PEG 3350. All crystals were grown at20° C. by sitting drop vapor diffusion. For cryo-protection, allharvested crystals were briefly incubated in the reservoir solutionssupplemented with 20% glycerol prior to be flash-frozen in liquidnitrogen. All diffraction data were collected at 24-ID beamline at theAdvanced Photon Source, and were processed with XPD and HKL2000 suite.

Structure determination and refinement. K-Ras/RDA1/GMP-PNP complexcrystallized in the space group of P21 with four molecules in theasymmetric unit. K-Ras/RDA2/GMP-PNP complex also crystallized in thespace group of P21 but with a single molecule in the asymmetric unit.Both structures were determined by molecular replacement with PHASERusing the previously determined K-Ras structure (PDB access 3GFT) as asearch model. RDA peptide models were built through iterative cycles ofmanual model building in COOT and structure refinement using REFMAC. Thefinal models were refined using PHENIX at 2.15 A and 1.7 A,respectively, and validated by MolProbity.

Live-cell confocal microscopy. Human tumor cell lines (e.g., H358 orHPAF-II) were seeded into LabTek II culture chambers in DMEM mediasupplemented with 10% fetal calf serum and grown overnight at 37° C.under standard cell culture conditions. The following day, media wasreplaced with media containing 5 uM of fluorescein-labeled peptide andincubated for 4 hours at 37° C. The cells were washed, stained withNucBlue Hoechst 33342 and Dextran 10k Alexa647, then imaged on aconfocal microscope. The fluorescent peptides were visualized with a 488nm laser and is shown in green in FIGS. 34A-B.

Example 1 Ras binding Peptides Characterization and Ras-Petide CrystalStructure

Binding Affinity. Binding affinity of the peptides to K-Ras wasdetermined by fluorescence polarization experiments. Below is thesequence of the peptides used along with their dissociation constantsmeasured.

Peptide Peptide Sequence K_(d) RDA1 GPRRPRCPGDDASIEDLHEYWARLWNYLYAVA17 nM (SEQ ID NO: 4) RDA2 GPRRPRCPGDDASIEDLHEYWARLWNYLYRVA  8 nM(SEQ ID NO: 5) RDA3 GRRPRRPRCPGDDASIEDLHEYWARLWNYLYAVA  6 nM(SEQ ID NO: 6)

Reduction Tests. This is an HPLC assay that can distinguish betweenoxidized (disulfide-crosslinked) peptide dimers from reduced(non-crosslinked) peptide monomers. By adding 5 mM or 50 mM DTT, areducing agent much stronger than the cellular environment, it wasobserved that the selenocysteine-containing peptide dimers cannot bereduced, unlike their cysteine-containing analogs (see FIGS. 31A-B).

Ras - RDA structures. FIG. 32 shows the overall structure, at 2.2Angstrom resolution. FIG. 32 also shows the primary helix and the keybinding residues identified.

Example 2 Yeast Display Screen for Ras-Binding Peptides

We pursued two strategies to identify peptides that bind the Raseffector domain, both of which involved screening large peptidelibraries by yeast surface display. Our first approach was to screennaive libraries that were based on a small peptide scaffold with noknown ability to bind Ras. These libraries were designed to contain asmuch structural diversity as possible, while remaining in a stableconformation. Our second approach was to screen a library based on thedomain of a protein known to bind the Ras effector domain. In this case,the goal of the screen was to identify a stabilized mutant of the domainthat was capable of binding Ras in the absence of the scaffoldingprovided by its parent protein.

Library Scaffold Selection. To identify candidate scaffolds for thenaive libraries, we searched the Protein Data Bank for polypeptides witha mass between 1000 and 5000 Da for which either an X-Ray or nuclearmagnetic resonance (NMR) structure was available. We manually curatedthe results to select peptides on the basis of structural stability,whether provided by noncovalent interactions or covalent ones (e.g.disulfide bonds). The helical avian pancreatic polypeptide (aPP, PDB:1PPT) was chosen for preliminary studies.

Avian pancreatic polypeptide (aPP) is a 32-amino acid miniproteinoriginally isolated from chicken pancreas. Its structure consists of anN-terminal polyproline type II (PPII) helix, a type-I β-turn, and aC-terminal a-helix. aPP forms head-to-tail homodimers in solution,stabilized by intermolecular contacts between residues from both thehelices and loops. Intramolecular hydrophobic interactions between thePPII and a-helices stabilize aPP monomers into a well-defined fold withrelatively high stability (melting transition (T_(m))≈62° C.), anattractive property for a scaffold since high thermal stability has beenshown to enhance the evolvability of some proteins. Schepartz andco-workers demonstrated that residues from the α-helices of variousproteins could be grafted onto the exposed face of the aPP α-helix toafford chimeric proteins that retained the ability to bind the originalprotein's targets. For example, Zondlo et al. grafted residues from theDNA-binding domain of the yeast transcription factor GCN4 onto the aPPscaffold to generate a miniprotein capable of binding the GCN4 half-sitewith low-nanomolar affinity. In another instance, Kritzer et al. graftedresidues from the hDM2-binding domain of p53 onto aPP, then appliedmutagenesis and screening to improve the affinity of the resultingpeptide.

Schepartz and co-workers also demonstrated that aPP could be endowedwith cell-penetrating properties by replacing multiple residues witharginines, which are known to enhance cell uptake in some contexts. Inone case, Daniels et al. substituted residues from the PPII helix andβ-turn with arginine to afford peptides that penetrated HeLa cells at aconcentration of 1 μM and were not sequestered in endosomes. In aseparate study, Smith et al. replaced residues from the α-helix witharginines to produce peptides that also penetrated HeLa cells at 1 μM,albeit with a significant fraction of peptides remaining localized toendosomes. This potential for cell penetration, along with the stablesecondary structure and established examples of engineering, made aPP anattractive scaffold for the screening and evolution of Ras-targetedlibraries.

An important caveat of these cell-penetration studies is that while theaPP mutants retained their aPP fold as determined by circular dichroism(CD) spectroscopy, they were destabilized by the introduction ofarginines. Because a less stable scaffold is predicted to tolerate fewermutations before losing its fold, a smaller fraction of the resultinglibrary would have a defined conformation. We therefore sought toidentify an aPP mutant that incorporated some of the argininesubstitutions that were shown to confer cell permeability, but that didnot compromise the stability in the scaffold. As our aim was to use thea-helical surface for randomization, we focused on the mostcell-penetrating peptide from the PPII-displayed arginine series, whichcontained six arginine mutations. Inspection of the aPP crystalstructure suggested that three of the mutated residues form potentiallystabilizing contacts with other amino acids within the peptide. To testthe hypothesis that these residues contributed to the majority of thedestabilization, we synthesized an aPP mutant, aPP-M, that left thesepositions unchanged (wild-type), while mutating the remaining three toarginine (see FIGS. 4A-B for sequences). To assess the stability of thispeptide, we recorded its CD spectrum and melting profile alongside thatof aPP (FIGS. 3A-B). We truncated both peptides after the 32^(nd) aminoacid, which is the end of the a-helix. The CD spectrum at 25° C. wasnearly identical for the two peptides and consistent with thosepublished in the literature, indicating that the overall conformationremained unchanged. Unexpectedly, the T_(m) of aPP-M was increasedrelative to aPP, from 64.5° C. to >77° C. The origin of this additionalstability is not entirely clear, although it is known that arginine canbe stabilizing in the context of PPII helices. Due to its improvedstability and arginine content, we used the aPP-M mutant as the scaffoldfor yeast display libraries.

The most practical way to cope with the instability of disulfide bondsin cells is to replace the disulfide with a more stable linker. Onepossibility would be to incorporate a diselenide bond, which isisosteric with a disulfide but has a redox potential that renders itstable to the reducing environment of human cells. Craik and co-workershave shown that such substitutions are able to improve the stability ofconotoxins without perturbing their structure. A second options would beto replace the disulfide with an unnatural linker, such as theall-hydrocarbon bridges used for “stapled peptides.” This couldpotentially be more stable than a disulfide or diselenide (as it cannotbe reduced) and may contribute to cell penetration, but would not be asisosteric. Additionally, there is no published precedent for stabilizing13 structures with such linkers, so there would likely be the need formethod development to optimize the synthesis, reaction conditions,linker length and composition, and so on.

Target Protein Preparation. Target proteins must be labeled for yeastdisplay studies so that they can be detected on the cell surface. Thisis typically accomplished by biotinylating the target protein and usingstreptavidin beads for magnetic activated cell sorting (MACS) orstreptavidin-fluorophore conjugates for FACS. One drawback of thisapproach is that peptides capable of binding streptavidin can producefalse positives, which can out-compete true target binders if theiraffinity is sufficiently high. Selection for these secondary-bindingsequences can be partially suppressed by utilizing different biotinbinding agents, for example, performing MACS with beads conjugated toanti-biotin antibodies, followed by alternating betweenneutravidin-phycoerythrin (NA-PE) and streptavidin-allophycocyanin(SA-PE) for FACS. For our initial library screens and directed evolutionefforts, we adopted this approach, although we did encountercontamination from secondary binders on several occasions. For our morerecent yeast display studies, we have attempted to avoid this issue byperforming FACS with Ras proteins that have been directly conjugated toa small-molecule fluorophore, with no accompanying secondary step.

To prepare the target protein, the gene for residues 1-177 of human KRas(G12V) was subcloned into a pET expression vector, with a nativeN-terminus and C-terminal His6 (SEQ ID NO: 55) and yBBr tags. The His6tag (SEQ ID NO: 55) enables the fusion protein to be purified from celllysate using standard immobilized metal affinity chromatography (IMAC)methods with Nickel-NTA or Cobalt resins. The yBBr peptide is anoptimized 11-amino acid substrate sequence (DSLEFIASKLA (SEQ ID NO: 94))for Sfp phosphopantetheinyl transferase, which can catalyze the covalentaddition of the phosphopantetheinyl group from Coenzyme A (CoA) onto thesidechain hydroxyl of the serine residue at position 2 in the peptide.This reaction generally tolerates substitutions at the sulfhydryl end ofCoA, and thus can be used to attach fusion proteins to conjugates of CoAwith biotin, fluorophores, etc with high selectivity (FIG. 6 ). Weviewed this strategy as preferable to nonspecific labeling, e.g. usingamine or thiol-reactive probes, which could potentially perturb thenative structure of Ras by modifying the lysine and cysteine residuesthat lie within or proximal to the effector domain. We chose the G12Vmutant of KRas for these studies since it is one of the most commononcogenic mutations found in human cancers, and has a lower backgroundrate of GTP hydrolysis than wild-type.

We expressed the KRas construct in E. colt (DE3) cells containing the T7lysozyme and the Rosetta I plasmid, which carries six tRNAs whose codonsare commonly found in human genes but are not present in E. colt. ThepET expression system works by placing both the recombinant protein(which has a T7 promoter) and T7 RNA polymerase under control of the lacoperator, which is constitutively suppressed by the lac repressor.Addition of isopropyl β-D-1-thiogalactopyranoside (IPTG, an allolactoseanalog) relieves the repression of these two proteins, permittingexpression of T7 RNA polymerase and thus the expression of therecombinant protein. We grew the cells in Lysogeny Broth (LB) media at37° C. until they reached an optical density (OD) of approximately 0.7,then induced expression of the fusion protein with IPTG at 30° C. Thecells were lysed by sonication, clarified by centrifugation, and Ras waspurified using Cobalt resin. The crude protein was further purified bygel filtration (FIG. 7A), enzymatically loaded with the desired guaninenucleotide (FIG. 7B), and then labeled with biotin or fluorophore usingSfp as detailed by Yin, J., et al. Site-specific protein labeling by Sfpphosphopantetheinyl transferase. Nat Protoc 1, 280-5 (2006). (FIG. 6 ).Labeling was verified by Matrix-assisted laser desorption/ionizationmass spectrometry (MALDI-MS) analysis of the protein before and afterthe Sfp reaction (FIG. 7C).

GTPases typically bind guanine nucleotides with high affinity; in thecase of HRas, the dissociation constant (K_(d)) is in the low-picomolarrange. Such high affinities mean that recombinantly expressed Rasproteins retain their nucleotides throughout the purification process,typically in a mixture of GDP- and GTP-bound states. Wild-type forms ofRas will slowly hydrolyze GTP to GDP even in the absence of GAPproteins, but mutants such as the G12V used in our studies tend tohydrolyze very slowly. This heterogeneous mixture is not ideal for yeastdisplay or biochemical assays, as the conformation and bindingproperties of Ras are markedly different between the two nucleotidestates. The high nucleotide binding affinity poses a challenge from thestandpoint of manipulation: proteins cannot be loaded simply byproviding a large excess of the desired nucleotide, and enzymes such asalkaline phosphatase are unable to efficiently degrade the nucleotidesbecause they are free in solution at concentrations far below the enzymeK_(m).

Two strategies have been developed to prepare homogenously loaded Rasproteins. The first involves the addition of EDTA to the purifiedprotein, which chelates Mg²⁺ ions and removes them from the nucleotidebinding pocket. This lowers the affinity of the Ras-nucleotideinteraction and allows nucleotides to be exchanged by adding a largeexcess (typically 100-fold) of the desired nucleotide and incubating atroom temperature.³⁴ In our experience, this method can load proteins upto a level of 85-90%, and was used to prepare proteins for our earlyyeast display and biochemical experiments. A second approach is to addalkaline phosphatase and non-hydrolyzable GTP analogs, such as Guanosine5′-[β,γ-imido]triphosphate (GppNHp) or β,γ-methyleneguanosine5′-triphosphate (GppCp) to Ras proteins that have been exchanged intobuffer that is Mg²⁺-free. Under these conditions, the Ras-nucleotideaffinity is sufficiently low to permit exchange of the initialnucleotide with the nonhydrolyzable analog, and if Ras is sufficientlyconcentrated (>100 μM) the concentration of hydrolysable nucleotidesbecomes high enough to be efficiently degraded by the alkalinephosphatase.³³ If GppCp is used, GDP or GTP can be efficiently loadedback on the protein following phosphatase removal, as GppCp has 100-foldlower affinity and is easily competed by an excess of naturalnucleotide.³⁵ This method can be used to achieve nearly quantitativeconversion to Ras proteins loaded with the desired nucleotide, and wasused for our more recent studies. We determined the Ras nucleotide stateby injecting purified proteins onto a reverse-phase (C18)high-performance liquid chromatography (HPLC) column equilibrated withphosphate buffer containing 7.5% acetonitrile and 100 mMtetrabutylammonium bromide. The tetrabutylammonium ions bind guaninenucleotides at a stoichiometry proportional to the number of phosphategroups, such that GTP is complexed with more lipophilic cations than GDPand thus behaves as a more hydrophobic molecule. Developing the columnunder isocratic conditions affords clear separation of GDP and GTP (FIG.7B), whose retention times can be determined using purified nucleotidestandards.

Yeast Display Screening. We carried out yeast display protocols asdescribed by Chao, G., et al. Isolating and engineering human antibodiesusing yeast surface display. Nat Protoc 1, 755-68 (2006). We firstperformed an initial pilot screen with the aPP library, usingbiotinylated KRas(G12V)-GTP as the target. As the size of the librarywas larger than the number of cells that can be conveniently evaluatedby FACS, we began the screen with a MACS step. We screened 2 * 10⁹ cellsat a Ras concentration of 1 μM, and isolated approximately 190,000cells. We sorted the resulting library by FACS for one round at 1.8 μM,then three rounds at 550 nM. These five sorts afforded a cell populationthat showed strong binding to Ras at 550 nM (FIG. 9 ). To test whetherthe displayed peptides bound the Ras effector domain, we incubated yeastwith KRas that had been pre-mixed with a large excess of the RBD of BRafThe apparent Ras binding was decreased, although some still appeared tobe bound. We sequenced the isolated population and found three closelyrelated peptide sequences (see FIG. 10 and discussion below).

Directed evolution of aPP-scaffolded peptides. FIG. 10 provides a listof peptides identified through the course of the evolution. Preliminarystudies were focused on three hits derived from the aPP-mutant library,which were named 221-1, 221-2, and 221-3. All three shared several ofthe randomized residues in common: H18, W21, W25, N26, and Y29 (FIG. 10). At the remaining positions, there was no strong consensus (E/G atresidue 15, A/E/W at residue 19, and A/Q at residue 23). We alsoobserved a spontaneous mutation at R6 to lysine in 221-3. We noted thatthere was a relatively high prevalence of hydrophobic residues in thesesequences, suggesting that the observed binding could be due to weaklyspecific hydrophobic interactions. To assess this possibility, weperformed yeast surface binding assays on the aPP hit population in thepresence and absence of human serum, which contains a heterogenousmixture of proteins and would be predicted to lower Ras-peptide bindingif the interaction was primarily driven by hydrophobic interactions. TheFACS plots showed essentially no change in binding even when serum wasadded to 10% v/v (FIG. 9 ), indicating that the Ras-peptide interactionis resilient to nonspecific competitors.

Directed evolution was used to improve the affinity of the aPP hits.Yeast display was done as before, using an initial MACS round followedby FACS, at a lower concentration of KRas. Additionally, we decided toconduct the evolution in the presence of 5% v/v human serum and 100μg/ml nonspecific DNA (single stranded, from salmon sperm) to maintain aselective pressure against nonspecific binding. The summary ofconditions and their resulting sequences is shown in FIG. 10 , withcolor-coding to indicate the round in which mutations first appeared.

For the second round (which afforded the 223 peptides), we diversifiedthe three 221 hits from the first round by error-prone PCR, thenperformed MACS at a KRas concentration of 100 nM. We enriched theresulting population over five rounds of screening by FACS at 50 nMKRas, affording two unique sequences that shared two mutations in common(P13S and V30A) along with an additional mutation each (X23R for 223-1and VI4I for 223-2). By inspection of the nucleotide sequences, we foundthat 223-1 was derived from 221-2, and that 223-2 was derived from221-1. It is important to note that one cannot assume that all of thesemutations are beneficial; it is possible that there are neutral ordeleterious mutations that were selected by virtue of their geneticlinkage to favorable ones. It seems reasonable in the case of these twosequences to conclude that S13 and A30 are favorable, as they aroseindependently from different parent sequences and remained fixed (withone exception) in the subsequent rounds of evolution.

For the third round (which afforded the 224 peptides), we diversifiedthe two 223 hits from the second round by error-prone PCR, thenperformed MACS at a KRas concentration of 25 nM. We screened theresulting library twice by FACS at 25 nM KRas, and obtained three uniquesequences. Nucleotide analysis indicated that 224-1, 224-2, and 224-3were derived from 223-1, and that 224-4 was derived from 223-2. The224-1, 224-2, and 224-3 peptides share a common Y7C mutation (seebelow), with 224-1 carrying an additional F20Y mutation and 224-2carrying the VI41 mutation observed earlier in 223-2. The sequence of224-4 is identical to 223-2, with the exception of an additional PRRinserted at the beginning of the PPII helix. This apparently favorablemutation was most likely introduced into the library by primer slidingduring the PCR, perhaps because the sequence immediately prior to theaPP peptide is repetitive (G₄SG₄SG₄ (SEQ ID NO: 95)).

We initially characterized the Y7C mutation found in 224-1, 224-2 and224-3 as an artifact, assuming that this cysteine (in the PPII helix)was improving the apparent affinity of the peptide by forming adisulfide bond with one of the surface-exposed cysteine residues inKRas. This assumption later proved to be incorrect (see Chapter 2), butfor the subsequent (fourth) round that afforded the 225 peptides, wedecided to remove both this mutation and the PRR extension from theparent library templates. We prepared the library by error-prone PCR ofa synthetic template prepared by the overlap extension method describedabove (FIG. 5 ). The template contained all of the mutations found inthe third round, with the exception of Y7C and the PRR extension, in ashuffled (combinatorial) format. We also increased the concentration ofKRas to 100 nM, to avoid overly-stringent conditions that might enrichrare clones that contained the Y7C mutation. After one rounds of MACSand two rounds of FACS at 100 nM, 9 of 11 clones corresponded to the225-1 sequence, with a single clone containing an E19A mutation (225-5)and a single clone containing the A30P mutation (225-6). Note that thenumbering for this round is non-chronological, due to a record-keepingerror. None of the clones contained the Y7C mutation.

For the fifth and final round (which afforded the 226 peptides), weprepared the library as before by error-prone PCR of the hit templates.Following one round of MACS at 100 nM KRas, we performed three rounds ofFACS with decreasing the KRas concentration, starting at 100 nM, thenproceeding to 50 nM and finally to 20 nM. This population containedseven unique sequences, five of which contained the Y7C mutation,including one identical to 224-1 (226-4). Of the remaining two, one wasidentical to 225-1 (226-1) and the other was identical except for anI14V reversion. Based on these sequences, we concluded that we hadreached the point where improvements in affinity appeared to require theacquisition of a cysteine, at least given the library diversity that wasaccessible to our error-prone mutagenesis approach. We decided to stopthe evolution at this point and more thoroughly characterize ourpeptides in vitro. Because the 225-1 sequence was the most common clonein the 225 round, and appeared again without a cysteine in the 226round, we chose it as the representative peptide for these studies. Wealso decided to test a version of 225-1 that contained the PRR extensionfound in 224-4, reasoning that it may provide improved affinity andpotentially cell penetration. We named this peptide 225-3.

Example 3 In vitro Characterization of Ras-binding Peptides

From the directed evolution efforts, we selected two aPP-derivedpeptides, 225-1 and 225-3, for further study. These peptides bound KRasat nanomolar concentrations in the yeast display system, competed withRas for Raf binding, and were remarkably tolerant to the presence ofblocking agents (DNA and serum). This example describes the recombinantproduction of these peptides in E. coli, characterization of theirbinding properties in vitro, and initial efforts towards defining theirbinding site on the Ras surface.

Expression and Purification of 225 Peptides. During the course of thedirected evolution experiments, we prepared a small number of aPPpeptides (mostly from the 223 and 224 series) using solid-phase peptidesynthesis, as was done by Schepartz and co-workers for their studies(see Daniels, D. S. and Schepartz, A. Intrinsically cell-permeableminiature proteins based on a minimal cationic PPII motif. J Am Chem Soc129, 14578-9 (2007); Kritzer, J. A., et al. Miniature protein inhibitorsof the p53-hDM2 interaction. Chembiochem 7, 29-31 (2006); Smith, B. A.,et al. Minimally cationic cell-permeable miniature proteins viaalpha-helical arginine display. J Am Chem Soc 130, 2948-9 (2008)).However, due to the length of these sequences, and the prevalence ofresidue pairs that are challenging from a coupling standpoint (e.g. RPand RR), these syntheses were laborious and costly, and it was sometimesdifficult to obtain clean samples even after multiple rounds of HPLCpurification. Given that these peptides are composed entirely ofnaturally occurring amino acids, we sought to develop a recombinantexpression system to overproduce our aPP peptides in E. coli. Thisapproach has a number of advantages for sequences of this length,provided the yield is sufficient: protein expression in bacteria isgenerally less expensive and time-consuming than solid-phase synthesis,and the relatively low rate of translation errors⁴ is such that closelyrelated side products are less prevalent, although there are manyunrelated cellular proteins that must be purified away. We subcloned anE. coli codon-optimized fragment encoding the 225-1 and 225-3 peptides(see FIG. 11 for sequences) into a pET30a expression vector, whichcontains an N-terminal His6 tag (SEQ ID NO: 55) and S-tag, and placed atobacco etch protease (TEV) cleavage site immediately prior to the startof the peptide sequence. At the N-termini of the peptides, we added aGCG tripeptide to act as a flexible linker between the TEV site and thestart of the PPII helix (to promote efficient proteolysis) and toprovide a handle (cysteine -SH group) to allow labeling of the peptideswith fluorophores and biotin for subsequent experiments.

We transformed these constructs into BL21 Rosetta pLysS cells, whichwere grown in LB with antibiotics to maintain the plasmid, and inducedexpression at 30° C. using IPTG, as described for the purification ofthe Ras proteins. Following induction, we harvested the cells bycentrifugation, lysed them by sonication, and purified the His-taggedpeptide fusion using cobalt affinity chromatography. We cleaved theeluted protein by addition of TEV, then purified the resulting reactionby HPLC.

Representative data for the purification of the 225-1 peptide are shownin FIGS. 12A-C. The 225 peptides absorb strongly at 280 nm due to thetwo tryptophan and four tyrosine residues, and the HPLC trace of the TEVreaction shows a strong peak at 11 minutes (FIG. 12A) that contains thecleaved peptide with no apparent contamination when analyzed by liquidchromatography-mass spectrometry (LC/MS) (FIGS. 12B-C). Followingpurification, the peptides were dissolved in dimethyl sulfoxide (DMSO)and their concentration was determined by measuring the Am in a mixtureof 50% DMSO and 50% phosphate buffer (pH 7.5), using an extinctioncoefficient predicted by the amino acid sequence and an experimentallydetermined correction factor (0.91) for this particular solventcombination.

The yields of 225-1 and 225-3 obtained with this expression system weremodest, typically on the order of ˜50 nmol (˜220 μg) for a two-literprep, which was sufficient material for preliminary studies. However,our subsequent efforts to express point mutants for alanine scanning(see section III.E) were much more poorly expressed, sometimes requiring6+ liters of culture and, in the case of some mutants, affording noexpression at all. Due to the relatively hydrophobic nature of thesequences, we hypothesized that co-expression with molecular chaperonesmight improve the peptide yield. We therefore expressed our constructsin BL21 cells carrying a modified form of the pG-KJE8 plasmid (Clontech)which carries the dnaK, dnaJ, grpE, GroEL, and GroES chaperones undercontrol of an arabinose-inducible promoter. Inducing with IPTGaccompanied by 200 mg/l of arabinose dramatically improved the yield formost of the mutant peptides tested, allowing us to prepare sufficientquantities of all the alanine point mutants for biochemical studies.Co-expression with chaperones also improved the yield of the 225-1peptide (albeit more modestly), and this approach was adopted for theproduction of all subsequent peptides.

For experiments that required functionalized peptides, we labeled thecysteine near the N-terminus with maleimide conjugates (e.g.FITC-maleimide or Biotin-PEG₂-maleimide). We first treated the purified225 peptides with tris(2-carboxyethyl)phosphine (TCEP), a reducing agentthat lacks thiols and is less likely to react with sulfhydryl-reactivemolecules such as maleimides. The peptides were then labeled with theappropriate maleimide conjugate at room temperature, followed bypurification by HPLC and characterization by LC/MS as for the unlabeledpeptides. We typically performed these reactions in a mixture of DMSOand pH 7 buffer, to aid the solubility of the reactants and to ensurethat the pH was conducive to selective labeling of the maleimide groupsby the cysteine.

Upon attempting to dissolve the 225-1 and 225-3 peptides in buffer, wefound that 225-1 had relatively good solubility (up to ˜100-200 μM atneutral pH), whereas the 225-3 peptide was not soluble at neutral pH andcould only be solubilized at micromolar concentrations at low (<5) orhigh (>11) pH. However, preliminary testing indicated that the 225-3peptide possessed a stronger binding affinity than 225-1, and was alsosomewhat cell permeable. We therefore conducted the majority of thefollowing experiments using 225-3, and used 225-1 only in instanceswhere high concentrations at neutral pH were required (e.g. NMR).Because the difference between these two peptide sequences is relativelyminor, and because they exhibit similar binding affinities, CD spectra,and inhibition of nucleotide dissociation from Ras, we will generallyrefer to them as the 225 peptides.

Characterization of Peptide Secondary Structure by Circular Dichroism.The 225 peptides contain 12 amino acid substitutions relative to aPP-M,and 15 compared to aPP. Most of these changes occur in residues notpredicted to contribute to the aPP fold (based on inspection of thecrystal structure); however, with nearly half of the amino acids mutatedfrom aPP to the 225 peptides it was not obvious that their conformationswould be the same. To gain an initial insight into the secondarystructure of the 225 peptides, we recorded CD spectra of 225-1 and225-3. The 225-1 peptide was readily soluble in buffered phosphate at pH8, but the 225-3 peptides could only be prepared at sufficiently highconcentration for CD studies at pH <5 and pH>11 (see above). Wetherefore recoded the CD for 225-3 at pH 4.5 and pH 12. The data areshown in FIGS. 13A-B. The 225 peptides have CD spectra similar to thatof aPP-M, although the two minima (typically at 208 nm and 222 nm fora-helices) appear to be slightly red-shifted for the 225 peptidescompared to aPP-M. In addition, the relative intensities of the minimaare different: whereas aPP-M has nearly identical CD at 208 nm and 222nm, the 225 peptides have stronger CD at 225 compared to 210. In thecontext of a-helices, increased [θ₂₂₂]/[θ₂₀₈] ratios are oftenassociated with the transition from noncoiled helices to coiled coilstructures.⁵ These data suggest that the 225 peptides may form a similartype of structure in solution; one possibility is that they are moreprone to form head-to-tail homodimers (as has been reported for aPP)than their aPP-M parent.

To gain insight into the stability of the 225 peptides, we recorded theCD at 222 nm from 10° C. to 90° C. The melting curves show sigmoidaltransitions for the three 225 peptide samples tested; for 225-3, pH 12(T_(m) of 46.2° C.) appears to destabilize the fold compared to pH 4.5(T_(m) of 57° C.), and at neutral pH, 225-1 has a T_(m) of 66.6° C. ThisTm for 225-1 is lower than for the aPP-M parent (T_(m)>77° C.), butstill higher than that of wild-type aPP (T_(m) of 64.5° C.). Thisrelatively high melting transition suggests that the 225 peptides arethermally stable. Although a detailed understanding of the peptideconformation requires more direct structural information (e.g. from NMRor X-ray crystallography), these CD data, along with the fact thatnearly all of the residues known to contribute to the aPP fold wereconserved during the course of our evolution, suggests that the 225peptides likely share a similar structure as their aPP parent.

Quantification of the Ras-Peptide Binding Affinity by FluorescencePolarization. The yeast display system suggested that the 225 peptideswere capable of binding the Ras proteins at mid-to-low nanomolarconcentrations. To gain a more quantitative measure of the Ras-peptidebinding affinity, we conducted fluorescence polarization (FP) assayswith 225 peptides that had been labeled with fluorescein isothiocyanate(FITC). This assay relies on measuring the fluorescence in both theplane that is parallel to the excitation light and the planeperpendicular to it, such that FITC-labeled peptides with relativelyslow tumbling in solution will exhibit higher anisotropy than those thattumble quickly. As the 225 peptides are significantly smaller than theRas proteins (4.5 kDa compared to 21 kDa), the transition from a freepeptide in solution to a Ras-bound peptide is predicted to exhibit anincrease in the fluorescence polarization. We measured the FP of the225-3 peptide at varying concentrations of KRas (G12V)GppNHp anddetermined a dissociation constant (K_(d)) of 20 nM (FIG. 14 ). Thisaffinity is comparable to that of HRas for the B-Raf RBD, and is twiceas strong as that of KRas for the B-Raf RBD.⁷ The hill coefficient forthis binding curves was 1.0, suggesting that the binding isnon-cooperative. We noted that these FP experiments routinely producedmessy data, and many replicates were required to obtain clean curves,although the affinity was reproducibly in the range we report here. Thiswas particularly true of peptides from the 225-1 series (i.e. those thatlacked the N-terminal PRR extension, see Chapter I). We thereforeproceeded to perform the remainder of the FP experiments with 225-3 andits derivatives.

We next measured binding curves for the 225-3 peptide and the GDP formof KRas (G12V), as well as the GppNHp and GDP forms of KRas (WT). Themutation state of Ras did not appear to have a strong effect on thepeptide binding affinity, whereas the GppNHp nucleotide state wasslightly preferred over the GDP state for both proteins. The nucleotideselectivity observed for these peptides is significantly less than thatof naturally occurring Ras-binding proteins, which typicallyexhibit >100-fold selectivity for the GTP state. However, these proteinshave evolved to possess this property, whereas we included no explicitselectivity requirement during our initial directed evolution effort. Inmore recent yeast display experiments, we have attempted to improve thenucleotide selectivity by screening for peptides with higher ratios ofbinding to KRas.GTP vs. KRas GDP (see Chapter 3).

The three Ras proteins are all capable of binding most Ras effectors,with only slight differences in affinity for the Raf RBD.⁷ To determinethe isoform selectivity of the 225-3 peptide, we performed FP with theGppNHp-bound forms of KRas, HRas, and NRas (FIG. 14 ). The K_(d) of225-3 for KRas (20 nM) is only slightly higher than that for HRas andNRas (45 nM), indicating that all three Ras isoforms bind the 225-3peptide with similar affinity.

The Ras proteins belong to a large family of GTPases, some of whichshare significant structural and sequence similarity to Ras. As a numberof these proteins are involved in housekeeping functions across manycell types, an important property of a Ras inhibitor is the ability todiscriminate between the Ras proteins and their close family members. Todetermine the selectivity of the 225 peptides, we performed FP assayswith GppNHp-bound Rap1a, RalA, and Rab25, which all share the sameGTPase fold as the Ras proteins. Rapla and RalA were selected becausethey are the two proteins closest in primary sequence to the Rasproteins, whereas Rab25 belongs to the distantly related Rab proteinfamily with less than 30% sequence identity to Ras.⁸ Rapla was ofparticular interest to us because it is capable of binding some Raseffectors, including the Raf RBD, and some Rap effector proteins are inturn capable of binding Ras.⁹ RalA and Rap25 did not bind 225-3 to anappreciable extent, with a Ka of ˜10 uM for Rab25 and >10 μM for RalA(FIG. 14 ). Rapla appeared to bind 225-3 with slightly higher affinity(3.5 04), but was still more than 100-fold weaker than Ras. These datasuggest that the 225-3 peptide has remarkable specificity for the Rasproteins over closely related family members, despite the lack of anexplicit selection for specificity during the evolution experiments.

Quantification of the Ras-Peptide Binding Affinity by SPR. To obtain anindependent measure of the Ras-peptide binding affinity, we performedbinding assays using surface plasmon resonance (SPR, often referred toas Biacore). This assay involves immobilizing a molecule of interest onthe surface of a gold wafer, and directing polarized light through aprism to the wafer. This is done under conditions of total internalreflection, in which the intensity of the light reflected from thesurface is dependent on the refractive indices of the materials oneither side of the gold surface. Relatively small changes at thesurface, such as binding of a biomolecule to the immobilized ligand,alter the refractive index and result in a change in the intensity ofthe reflected light. SPR systems work by immobilizing a molecule ofinterest on the gold wafer, then flowing a second molecule over the chipwhile continuously recording the reflected light. A binding eventbetween the immobilized and “free” molecule is detected as an increasein resonance units (RU) and can be used to measure both the kinetic andthermodynamic parameters of binding events. One advantage of this methodis that the “free” molecule is detected purely by its mass, and thusdoes not require any labeling. The immobilized molecule may be capturedon the chip covalently (e.g. by nonspecific coupling of amino or thiolgroups) or noncovalently (e.g. with a biotin-streptavidin pair).

Our initial approach was to immobilize the 225 peptides on the chipsurface and flow free, unlabeled Ras proteins over it. The advantage ofthis setup is that the Ras proteins are —5 times larger in mass than thepeptides, and are thus expected to produce a stronger signal uponbinding since the RU signal detected by the SPR system is roughlyproportional to mass. We selected a streptavidin-functionalized goldchip and immobilized 225-3 peptide that had been biotinylated at thecysteine handle (see above). The peptides were captured successfully onthe chip as determined by an increase in the baseline RU signal, butupon adding unlabeled Ras protein, no appreciable increase in bindingsignal was observed. The cause of this was not immediately apparent; ourinitial assumption was that the biotinylation somehow rendered thepeptide incapable of binding Ras, or that the Ras-peptide binding wasnot compatible with the biotin-streptavidin binding (e.g., for stericreasons). However, this explanation was not consistent with pulldownassays in which the same biotinylated 225-3 peptides were successfullyused to bind both purified KRas and Ras from cell lysates usingstreptavidin beads (see FIGS. 18A-B).

Given our knowledge at the present, we can account for theseobservations with the peptide-dimer model: upon introducing thebiotinylated peptides to the streptavidin chip, the extremely highaffinity of the biotin-streptavidin interaction (-50 fM)¹° led all ofthe biotin moieties to become immobilized. Streptavidin is ahomotetrameric protein with four biotin-binding sites, and by inspectionof the crystal structure, it was apparent that the two peptides couldnot plausibly engage adjacent biotin-binding sites while remaining in ahead-to-tail aPP-like homodimer structure. Because thebiotin-streptavidin interaction is essentially irreversible on thetimescale of these experiments, it is likely that the homodimers wereeffectively torn apart upon introduction to the streptavidin chip, andthus were immobilized in a state that was incapable of binding the Rasproteins. We note that this explanation makes the following prediction:immobilization of biotinylated peptide, followed by incubation withunlabeled peptide, should result in the formation of dimers on the chipsurface that are capable of binding Ras.

At the time of these experiments, the cause of this phenomenon remainedunresolved, and we proceeded with the alternate SPR strategy ofimmobilizing the Ras proteins and flowing free peptides over thesurface. We used Sfp-biotinylated Ras proteins as described in Chapter Ifor yeast display, testing both the GppNHp- and GDP-bound states. TheRas proteins could be stably captured on the chip, and exhibited stablebinding to the unlabeled 225-3 peptide (FIGS. 15A-B). SPR affinityexperiments are typically performed in one of two ways: “multi-cycle”runs, where protein is immobilized, a single injection of ligand isflowed over the surface, and the chip is subsequently regenerated sothat a new batch of protein and ligand can be introduced, and“single-cycle” runs, where the protein is immobilized and multipleinjections are performed in series. Single-cycle runs are faster andmore cost-effective than multi-cycle runs, and afford accurate dataprovided the off-rate of the binding event is slow relative to theon-rate (i.e. when the binding affinity is high), and was the method weused for our studies.

Both the GppNHp and GDP states bound 225-3 with high affinity, affordingdissociation constants of 2.5 nM and 0.46 nM, respectively. It isapparent both by visual inspection of the curves and by the calculatedkinetic parameters that the dissociation is slower for the GDP state ofRas than GTP, an observation that is consistent with off-rate selectionexperiments we have performed using yeast display. We found that bothcurves were best fit by a two-step binding model, which did not matchour expectations, and the results of these experiments also disagreedsomewhat with those from fluorescence polarization: the calculatedaffinities were an order of magnitude higher than those found by FP, andthe nucleotide selectivity was reversed.

The precise cause of these discrepancies are not entirely clear to us,although the peptide-dimer model may offer some insight, as it predictsthat there should be multiple interdependent equilibria present withinthe system. Since the peptide is prepared at varying concentrations(from 1-100 nM) and injected over the immobilized chip, higherconcentrations of peptide would experience a stronger effective Ka forRas since a greater proportion of peptides would be present in thedimeric (Ras-binding) state. This may result in a distortion of thebinding curves and data fitting since the concentration of peptide addedmay not accurately reflect the effective concentration of peptide dimeravailable to bind Ras. In FP experiments, the peptide is held at aconstant concentration and thus may be less susceptible to this effect;however, as the FP is expected to be different for the monomericpeptide, the dimeric peptide, and the Ras-peptide dimer complex, it isalso likely that multiple states are contributing to the bulk FP signal.Both of these binding assays thus possess caveats that restrict theconclusions that can be drawn from them, and it is probably safest toassert simply that the peptide-Ras interaction is in the mid-to-lownanomolar range.

Alanine Scanning Mutagenesis of the 225-3 Peptide. We next sought togain a more detailed understanding of the Ras-peptide interaction. Asdiscussed above, our CD and evolution results suggested that the 225peptides retained the general fold of aPP, but the peptide residuesinvolved in Ras binding were not readily apparent. Because the aPPlibrary was diversified on the outward face of the a-helix, and becauseessentially all of the mutations that appeared during the evolution werelocated in this region, it is tempting to speculate that the 225peptides engage Ras primarily through residues on its a-helix. To testthis hypothesis, we performed alanine scanning mutagenesis by testingvariants of 225-3 that each contained a single alanine point mutation.Alanine is the most common amino acid used in this type of experimentbecause it is small, yet mimics the conformational preferences of mostamino acids. Alanine is particularly suitable for this peptide inparticular because it is generally stabilizing in both PPII anda-helices, which likely constitute the majority of the 225 peptidesecondary structure.

We selected 10 residues for mutagenesis: two in the PPII helix, two inthe loop, and six in the a-helix (see FIG. 16 ). The plasmids for thesemutants were constructed using site-directed mutagenesis PCR andexpressed and purified as described above. Of these, nine could beexpressed and purified, although some of these were absolutely dependenton co-expression with chaperones. Only one mutant, EISA, could not beexpressed, even in the presence of chaperones. This residue is on thea-helix and is predicted to be outward-facing, and the peptide-dimermodel does not predict any interactions between this residue andresidues on the neighboring peptide, so the reason for this poorexpression is not presently clear.

Once purified, the alanine mutants were labeled with FITC and tested byFP (FIGS. 17A-C). The typical expectation for an alanine scan is to findsome mutants that affect the property being studied, and others thathave little or no effect. Unexpectedly, every mutant tested disruptedbinding by at least four-fold, and most caused at least a 10-foldreduction in measured affinity. Three of these mutations (I14A, W21A,and W25A, all on the a-helix) appeared to have a significantdestabilizing effect on the peptide secondary structure as assessed byCD. Our initial interpretation of these data was that the other sevenresidues were all involved in binding to Ras, suggesting that thepeptide engaged Ras not just though the a-helix but by presenting one“side” of the peptide with contacts from both the PPII and a-helices. Inlight of the peptide-dimer model, these data suggest an alternativeexplanation: that some of the residues tested contact Ras, whereasothers are involved in stabilizing the dimer. Indeed, inspection of theaPP dimer structure (FIGS. 23A-C) shows that several of the residuestested are likely involved in forming contacts between monomers: thePPII helix (which contains two arginines that appeared to stabilizebinding) is in close proximity to a patch of acidic residues on theopposing peptide, and the pair of W21 residues (which are Tyr in aPP)appear to be in an appropriate distance for i-stacking with each other.Thus, the interpretation of the alanine scan is somewhat complicated byour inability, given these data, to distinguish between residues thatdirectly engage Ras and residues that stabilize the peptide-peptidedimerization. Additionally, it should be noted that since the peptidesare in a homodimer, the alanine scan mutants did not interrogate therole of a single residue but rather a pair of residues.

When performing assays with biologically active molecules, it isvaluable to have a negative control molecule that is as similar aspossible to the active compound while lacking some or all of the targetactivity. In the context of our studies, this would ideally be a 225peptide with a single mutation that abrogates binding to Ras, withoutdisrupting the peptide structure. From the alanine scan series, threepeptides had Ka values exceeding 5μM: W21A, W25A, and N26A. As discussedabove, both of the tryptophan mutants appeared to be destabilizedcompared to the 225-3 parent as judged by CD. However, the N26A mutanthad a CD profile that was unchanged compared to 225-3, and we thereforeselected this peptide for use as a negative control in our subsequentstudies.

Pulldown Assays in Cancer Cell Lysates. The data thus far indicate thatthe 225 peptides bind the Ras proteins with nanomolar affinity and goodspecificity. All of these experiments were performed with recombinantlyexpressed Ras proteins, however, and it remained possible that theseproteins did not accurately reflect the nature of Ras in living cells(due to posttranslational modifications, differences in fold,participation of partner proteins, etc). To test whether the 225peptides were capable of binding the endogenous Ras proteins in cancercells, and whether they could disrupt the binding of these endogenousproteins with effectors, we performed pulldown assays in lysates of theCapan-1 pancreatic adenocarcinoma cell line, which harbors a mutant formof Ras (G12V) and has been shown to be dependent on Ras activity forsurvival.

We grew the cells with standard methods and lysed them in nondenaturingconditions (buffer containing 1% v/v of the nonionic detergent TritonX-₁₀₀, see Methods for additional details). We incubated the lysate withbiotinylated 225-3 peptide, biotinylated 225-3 N26A peptide, or DMSOcontrol, then captured the peptides with magnetic streptavidin-coatedbeads and ran the samples on a sodium dodecyl sulfate-polyacrylamide gelelectrophoresis (SDS-PAGE) gel, followed by transfer to a nitrocellulosemembrane and western blotting for Ras. To test whether these peptideswere capable of competing with Ras effectors, we performed in parallelthe same set of experiments with lysates that had been pre-incubatedwith an excess of the Raf RBD. This treatment is expected to result innearly all Ras molecules being bound to Raf (due to the high Ras-Rafaffinity), and if Raf and the 225 peptides share a binding site, theprediction is that the amount of Ras pulled down by the peptides will bediminished.

The results of this experiment are shown in FIG. 18A. The lysatecontained a significant amount of Ras as judged by the input lane, butRas was not pulled down by beads alone, nor by beads in the presence ofthe N26A mutant of 225-3. The active form of 225-3 pulled down Ras, butnot when the lysate was pre-incubated with the Raf RBD. These datademonstrate that the 225 peptides are capable of binding endogenous Rasin human cancer cell lines, and that the peptides appear to share abinding site with Raf, suggesting that the 225 peptides may be capableof inhibiting Ras effector binding in vivo.

It is possible that this apparent competition was not the result of Rafand 225-3 sharing overlapping binding sites, but was instead due to theability of Raf to sequester Ras in aggregates, or block the biotinbinding sites on the beads, and so forth. As a control experiment, wereversed the pulldown strategy and instead captured the Raf RBD, whichis tagged with glutathione-S-transferase (GST), using glutathione beads.This assay is often used to determine the Ras activity status in cancercells,¹⁴ as only the GTP-bound form of Ras can bind Raf with appreciableaffinity. Ras was not pulled down by glutathione beads alone, but was inthe presence of GST-tagged Raf, and pre-incubation with the N26A mutantof 225-3 did not disrupt this pulldown, whereas 225-3 abrogated itcompletely (FIG. 18B). This confirms the results of II-9A, indicatingthat the 225 peptides are capable of competing with a canonical Raseffector for binding to endogenous Ras.

Identification of the 225 Binding Site on Ras. The pulldown data shownabove suggest that the 225 peptides bind at or near the Ras effectordomain, as they are capable of competing with Raf proteins for Rasbinding. However, it is also possible that this competition is theresult of an allosteric mechanism, where Raf and the 225 peptides bindnonoverlapping sites but engage distinct conformations of Ras that aresufficiently different as to prevent the other ligand from bindingsimultaneously. We therefore sought to define the precise 225 peptidebinding site on the Ras surface. One characteristic of Ras effectorproteins is their ability to interfere with dissociation of guaninenucleotides from the nucleotide binding pocket on Ras. To assess whetherthe 225 peptides share this property, we performed a Ras nucleotidedissociation assay originally reported by John and co workers ¹⁵ whichrelies on fluorescent analogs of guanine nucleotides. We synthesized theN-methylanthraniloyl ester of GppNHp (mantGppNHp), whose fluorescence isknown to increase upon binding Ras.

We performed nucleotide dissociation inhibition assays in a mannersimilar to the classic ³²P-labeled nucleotide experiments that involveadding “cold” nucleotide to proteins bound with “hot” nucleotide. KRaswas loaded with mantGppNHp using alkaline phosphatase as described forRasGppNHp, then incubated with peptide, Raf RBD, or nothing beforeadding a large excess of GppNHp. This excess of unlabeled nucleotideeffectively renders the dissociation of mantGppNHp irreversible, andthus the dissociation rate constant can be measured by fitting thecurves to an exponential decay (FIG. 19 ).

In the absence of additional “cold” nucleotide the fluorescence levelwas relatively stable, indicating that photobleaching, proteinunfolding, etc. did not lead to a significant reduction in signal overthe timecourse of the experiment. Upon adding an excess of GppNHp, thefluorescence decreased in an exponential fashion, and this was abrogatedby the introduction of the Raf RBD, as had been previously reported.¹⁵The addition of either 225-1 or 225-3 had a similar effect, slowing theapparent rate of nucleotide dissociation to a level comparable with thatof the Raf RBD, but addition of 225-1 N26A or 225-3 N26A did notdecrease the rate of dissociation, indicating that this effect wasdependent on binding to Ras. Thus, the 225 peptides appear to inhibitthe dissociation of nucleotides from Ras, suggesting that either theirbinding site overlaps with the nucleotide binding pocket or that peptidebinding restricts the protein from accessing conformations with lowernucleotide affinity.

To develop a more granular understanding of the Ras-peptide interaction,we performed solution NMR experiments to identify the residues on eachmolecule that were involved in binding. The method we used was ¹H-¹⁵Nheteronuclear quantum spin correlation (HSQC) spectroscopy, an NMRtechnique that detects chemically distinct N-H bonds (in the case ofproteins, primarily the amide N-H bond) in a molecule and produces a 2Dplot of crosspeaks, located according to the individual shifts of theproton and nitrogen atoms in the N-H pair (see e.g. FIGS. 20A-C). Due tothe variability in chemical environment throughout the protein, most N-Hbonds can be distinguished from one another under the proper conditions,and with the aid of several additional measurements (such as ¹H-¹³CHSQC, HCCH TOCSY, and so on) the ¹H-¹⁵N HSQC crosspeaks can be assignedto specific residues within the protein. If these assignments are known,changes in the protein conformation upon binding a ligand can be mappedto specific sites within the protein by comparing the HSQC spectra inthe presence and absence of the ligand and identifying the crosspeaksthat shift.

The assignments for KRas(WT) GDP were published in 2012, enabling us toperform HSQC studies without assigning the Ras protein de novo. Weexpressed the KRas protein in E. coli as before, but using minimalsynthetic media with ¹⁵NH₄Cl as the sole nitrogen source. This proteinwas purified, exchanged into the buffer reported for the NMR assignment,then ¹H-¹⁵N HSQC measurements were performed on a Bruker 700 MHz NMRspectrometer equipped with a cryoprobe. For these studies, we usedtransverse relaxation optimized spectroscopy (TROSY), a variant of thestandard ¹H-¹⁵N HSQC experiment that improves the quality of HSQCsignals from relatively large proteins.

The ¹H-¹⁵N HSQC spectrum of ¹⁵N-labeled KRas is shown in FIG. 20A. Thismeasurement afforded clear, distinct crosspeaks that corresponded wellwith the spectrum reported previously. To identify residues on KRas thatexperienced a change in chemical environment upon peptide binding, werecorded the same measurement in the presence of unlabeled 225-1peptide, which lacks ¹⁵N and thus is not visible in the HSQC spectrum.As discussed above, we used 225-1 for these experiments because 225-3 isnot soluble at the concentrations required for preparing these NMRsamples (>100 μM). We found that between two and three equivalents ofpeptide (according to our absorbance-based quantification) were requiredto achieve saturation, an observation that did not make sense at thetime but can now be explained by the peptide-dimer model, which predictsa binding stoichiometry of 1:2 Ras:peptide. The HSQC spectrum of theRas-peptide complex is shown in FIG. 20B, and the free Ras andRas-peptide spectra are overlaid in FIG. 20C.

The overlay shows that a significant number of residues experience achange in chemical environment upon binding to Ras, as evidenced by thelarge number of crosspeaks that shift between the “free” and boundspectra. It is not possible to know the identity of the peaks in theRas-peptide spectrum without further measurements (necessitating ¹³C andpossibly ²H labeling), but by identifying the (assigned) peaks in thefree spectrum that shift, one can develop an initial picture of whichresidues are affected upon peptide binding. We manually tabulated thecrosspeaks in the free spectrum that shifted upon binding to peptide,then used the published assignments to map them to the crystal structureof Ras (FIG. 21 ). We found that these residues were located in awell-defined cluster on one face of Ras that shared considerable overlapwith the Ras effector domain, as defined by co-crystal structures of Rasin complex with effector proteins. Residues elsewhere on the Ras proteinappeared to be unaffected, as their corresponding crosspeaks in the HSQCspectrum did not shift to an appreciable extent. These data thus suggestthat the 225 peptide engage a specific binding site on the Ras surface,and that this site overlaps with the effector domain, consistent withthe ability of the 225 peptides to block effector binding.

We next sought to perform the analogous NMR experiment on the 225peptides, by comparing the HSQC spectra of ¹⁵N-labeled 225 in thepresence or absence of unlabeled Ras. The crosspeak assignments for thisprotein have obviously not been established, but given the relativelysmall size of the peptide (35 amino acids for 225-1) we anticipated thatperforming these assignments would be straightforward. First, weexpressed the 225-1 peptide in ¹⁵N-containing minimal media as for KRas,and recorded HSQC spectra for the free peptide in the same buffer usedfor the Ras experiments. This afforded a relatively clean spectrum,albeit with several crosspeaks that appeared to overlap one another(FIG. 22A). We then recorded HSQC spectra for the ¹⁵N-labeled 225-1peptide in the presence of KRas. Unexpectedly, this spectrum containeddouble the number of peaks as the peptide-only sample (FIG. 22B).

This observation cannot be explained by contaminating signal from theprotein, as KRas was unlabeled (the natural abundance of ¹⁵N is lessthan 0.5% of total nitrogen) and most of the new crosspeaks did notoverlay with either the free or peptide-bound Ras spectrum. These dataare also not consistent with partial saturation, as many of the peakspresent in the peptide-only spectrum are absent from the Ras-peptidespectrum. Another explanation is that the peptide is capable of bindingRas in two conformations. This is formally possible, but unlikely, giventhat the intensities appear fairly uniform for all of the crosspeaks inthe Ras-peptide spectrum. This would only be observed if the twoconformations were populated in roughly equal proportions, requiringthem to be of similar energies, which is improbable for two states thatare sufficiently different to cause distinct HSQC spectra.

An alternative explanation is that the Ras proteins contain two distinctbinding sites for the 225 peptides that can be occupied simultaneously.This is consistent with the presence of two crosspeaks for each aminoacid, and is also compatible with the observation that at least twoequivalents of peptide are required to saturate Ras. We initially deemedthis model unlikely, as the Ras HSQC experiments suggested a singlebinding site and the FP assays showed typical sigmoidal binding curveswith a hill coefficient of 1.0. However, upon recalling that aPP andsome of its relatives are capable of forming head-to-tail dimers insolution (FIGS. 23A-C), we considered the possibility that the 225peptides engaged Ras as a dimer. This is consistent with the ¹⁵N-labeledpeptide HQSC spectra: a head-to-tail homodimer is symmetric and thus thetwo monomers are predicted to experience identical chemicalenvironments, and thus possess identical ¹H-¹⁵N crosspeaks. Ras is notsymmetric, however, so upon binding Ras the peptide-dimer symmetry isbroken and the two monomers experience different environments, leadingto a splitting in the spectrum.

The crystal structure of aPP, which crystallizes as a dimer, is shown inFIGS. 23A-C. In light of this model, a number of previously confusingobservations make sense, as discussed in the previous sections of thischapter. Particularly interesting was the recurrence of the Y7C mutationduring the directed evolution efforts: by inspection of thecorresponding tyrosine in the aPP structure (FIG. 23C), it is apparentthat the Y7 residues on opposing monomers come within close contact(π-stacking in the case of aPP), and it is plausible that the presenceof cysteines at this position lead to the formation of a disulfide bondthat stabilizes the peptide dimer and thereby increases its affinity forRas.

The gold standard for the structural characterization of proteincomplexes is X-ray crystallography, which can provide a detailed andcomplete structure at atomic resolution. In collaboration withcrystallographers in the Verdine laboratory (Seung-joo Lee and Rou-JiaSung) we have attempted to crystallize the KRas-225 and HRas-225complexes, which were prepared as described for the KRas-225-1 complexesstudied by NMR. So far, we have had no success, but our efforts in thisarea are ongoing.

One implication of the peptide-dimer model is that the 225 peptides arenot fully optimized for binding to Ras. This is a consequence of theconstraints imposed by the peptide homodimer: each residue (andtherefore each mutation that was tested during the evolution) mustappear in two positions within the Ras-binding dimer, whereas the Rasprotein is asymmetric. Thus, it is likely that there are multiplepositions within the Ras-peptide binding interface where a favorableamino acid mutation is prohibited because it is not compatible with thecontext of the corresponding site across the peptide dimer. Thispredicts that peptide heterodimers may be capable of gaining affinityrelative to the 225 homodimer.

Example 4 Improving the Affinity and Specificity of the 225 Peptides

The peptide-dimer hypothesis proposed in Chapter II suggests that the225 peptides may not be fully optimized for binding to Ras, as Ras isasymmetric and thus likely has distinct preferences for contact residuesthat are constrained to be the same amino acid in the peptide homodimer.This chapter discusses our preliminary efforts to test the dimerhypothesis using yeast surface display, and to identify peptide mutantsthat can heterodimerize with 225-1 and bind Ras with improved affinityrelative to the 225-1 homodimer. We also discuss our efforts to identifypeptide mutants that possess improved selectivity for Ras.GTP vs.Ras.GDP relative to the 225 peptides.

Complementation of the N26A Mutant on the Yeast Surface. If thepeptide-dimer hypothesis is correct, one prediction is that there shouldexist peptide heterodimers with improved binding for Ras, due tooptimized contacts that are not possible in a homodimer. For example,there are likely a number of residues in the 225 peptides that form acritical contact in the context of one peptide-binding half-site on theRas surface. If this contact is sufficiently stabilizing that anymutation at this site abrogates binding, then the corresponding residueon the partner peptide will be constrained to be that same amino acid,even if a different amino acid would be preferable. The consequence ofthis fact is that the strongest peptide homodimer is likely to be thesequence that represents the best compromise between the amino acidpreferences at each half-site. If this is the case, then the 225peptides may be sacrificing potentially favorable interactions due tothe constraints of binding as a homodimer.

An alternative way to express this concept is that deleterious mutationsin the peptide are likely to have a stronger effect in the context ofone half-site than in the other. For instance, we had shown that theN26A mutation abrogates binding to Ras by at least 100-fold, but it isunlikely that the two N26 residues in the homodimer contribute equallyto this effect, given that they must experience different environmentsand engage distinct residues (since Ras is asymmetric). Provided thatthis mutation does not disrupt the actual dimerization of the 225peptides, it is more plausible that the N26A mutation has a significantdestabilizing effect at one half-site and a weak, neutral, or evenpositive effect at the other. If this were the case, it predicts that aheterodimer of 225-1 and 225-1 N26A should have significantly improvedbinding to Ras relative to a N26A homodimer.

A method for screening libraries of peptide heterodimers would greatlyimprove our ability to identify stronger Ras binders. Although thekinetics and thermodynamics of the 225 homodimerization are notpresently known, it occurred to us that if monomer exchange were rapidenough, it might be possible to conduct yeast surface display withheterodimers between 225 mutants (displayed on the yeast surface) and225-1 peptide (supplied in trans and allowed to exchange into aheterodimer with the displayed mutant). In light of the prediction thata 225-1 and 225-1 N26A should be capable of binding Ras better than a225-1 N26 homodimer, we sought to test this idea using yeast cellsexpressing either 225-1 or 225-1 N26A and providing free 225-1 or 225-1N26A peptide in trans. After some optimization, we found thatheterodimer formation appeared to be possible by pre-incubating theyeast cells with mid-micromolar concentrations of free peptide, followedby pelleting (to remove excess peptide) and subsequent incubation withRas (FIG. 24 ).

KRas, and this binding appeared relatively unaffected by pre-incubationwith free 225-1 or 225-1 N26A. Yeast cells expressing 225-1 N26A did notbind Ras at a detectable level, consistent with the in vitro data(Chapter II), nor did they bind when pre-incubated with free 225-1 N26A.However, when pre-incubated with free 225-1, these cells exhibitedstrong binding to Ras, consistent with the hypothesis that the 225peptides bind Ras as dimers. It is important to note that these dataonly show partial rescue of the 225-1 N26A mutant's ability to bind Ras,and thus cannot formally reject the possibility that the N26A mutant isequally deleterious to both half-sites. However, it is likely that ourdimer-exchange technique occurs incompletely: the peptides displayed bythe yeast are constrained to the cell surface, and thus the localconcentration of these peptides is high, meaning that homodimerizationof displayed peptides should be strongly favored over heterodimerizationwith free peptides in solution. Because we cannot determine whatfraction of surface-displayed peptides are present in homodimeric vs.heterodimeric form, it is difficult to quantitatively interpret theincrease in binding observed upon incubation of surface-displayed 225-1N26A peptide with free 225-1. However, there is no significant decreasein binding when the surface-displayed 225-1 peptide is pre-incubatedwith 225-1 N26A, which would not be expected if the heterodimer weresignificantly weaker than the 225-1 homodimer. It remains possible thatheterodimer formation was particularly inefficient in this specificcase, but given that the peptides are identical to those used in theconverse experiment, this seems unlikely. Thus, these experiments arguethat the 225 peptides can at least partly complement the loss offunction of the N26A mutations when bound in a heterodimer.

Identification of Heterodimers that Bind Ras with Increased Affinity.Encouraged by the observation that yeast surface display could be usedto present heterodimers, we performed a complementation screen toidentify mutant/225-1 heterodimers that bound Ras with higher affinitythan the 225-1 homodimer. The experimental approach was as described forthe N26A complementation studies, where we pre-incubated yeast cellswith 225-1 and pelleted before adding Ras. We selected a Rasconcentration of 5 nM, which affords very weak binding for 225-1 (FIGS.26A-B). For this experiment, we used a scanning mutagenesis librarybased on the 225-1 peptide that systematically varied adjacent pairs ofresidues throughout the sequence (FIG. 25 ). The theoretical librarysize of this library is approximately 12,400 members (in terms of aminoacid diversity), which is small relative to the library sizes that canbe transformed into yeast. However, this approach allows for thesystematic evaluation of mutations throughout the sequence, whereaslibraries designed by error-prone PCR tend to be biased towards certainsubstitutions and are unlikely to cover every amino acid mutation atevery site,' much less every possible amino acid pair at adjacent sites.We therefore considered this strategy to be a superior way of testingsequence space for this experiment.

Using the scanning mutagenesis library, we performed the complementationscreen at 5 nM KRas.GTP, and after three rounds of sorting, isolated apopulation that appeared to bind Ras more strongly than 225-1, in amanner dependent on pre-incubation with free 225-1 (FIG. 26A).Sequencing this population revealed it to be primarily composed of asingle clone with a S13C/I14E double mutation. Provided below arepeptide mutants with improved properties relative to 225-1. Forconsistency, residue numbers are reported using the positions in the aPPpeptide. Mutations are underlined.

Peptide Peptide Sequence 225-1 GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYAVA(SEQ ID NO: 8) 225-1 GCGGPRRPRYPGDDACEEDLHEYWARLWNYLYAVA S13C/I14E(SEQ ID NO: 9) 225-1 GCGGPRRPRYPGDDASIEDLHEYWARLWNYLYRVA A30R(SEQ ID NO: 10)

This mutation is interesting because we once again see the emergence ofa cysteine residue. In light of our prior hypothesis regarding the Y7Cmutation that was found in our initial evolution studies (that wehypothesize is involved in forming a disulfide bond between monomers),we wondered whether this mutation may also be improving the Ras bindingaffinity by stabilizing the dimer. This mutant can only bind Ras at 5 nMwhen pre-incubated with the 225-1 peptide; therefore, it is unlikelythat this cysteine is involved in forming a disulfide with thecorresponding cysteine across the dimer. Indeed, inspection of thestructure of the aPP dimer demonstrates that these residues are farapart and not expected to interact in the context of a formed dimer.However, we recalled that the free 225-1 peptide used in thesecomplementation studies contained a free cysteine at its N-terminus (forlabeling purposes), and the aPP dimer model predicts that this residuemay be capable of interacting with the C13 residue in the displayedmutant (FIG. 27 ). Thus, one explanation for the improved binding isthat the S13C/I14E double mutant forms a disulfide-stabilizedheterodimer.

If this hypothesis is correct, then blocking the cysteine on the free225-1 peptide should eliminate the improvement in binding. To test this,we alkylated the cysteine on the 225-1 peptide with iodoacetamide (asmall organic molecule with good selectivity for thiols, see FIG. 26B),then repeated the complementation experiment. Consistent with ourprediction, the improvement in binding to Ras was almost completelyeliminated with this peptide when compared to unlabeled 225-1. Thissuggests that the S13C/I14E double mutant may indeed show improvedbinding to Ras by forming a disulfide-stabilized heterodimer with 225-1.It remains possible that this effect is not due to disulfide formation,but is rather a consequence of perturbing the 225-1 structure by thealkylation. However, iodoacetamide is a relatively small molecule andthe N-terminal cysteine on 225-1 was previously modified with biotin andfluorophores without abolishing activity, so we consider thisexplanation unlikely.

Improving the Nucleotide Specificity of the 225 Peptides. As previouslydiscussed, we found that the selectivity of the 225 peptides for Ras.GTPvs. Ras GDP was relatively poor (and was different depending on thebinding assay used). Because Ras.GTP is the target of biologicalrelevance, we wondered whether there were 225-1 mutants that exhibitimproved selectivity for Ras GTP. One advantage of yeast surface displayis the ability to use multiple fluorescent channels, and thus multiplebinding agents, which enables multiparameter sorting. We thereforeperformed a yeast display screen in which we added Ras.GTP and Ras GDP,labeled with different fluorophores (Ras GTP was biotinylated anddetected with SA-PE, Ras GDP was directly labeled with Alexa647). Whencells displaying 225-1 were labeled with 500 nM each of Ras.GTP and RasGDP, we observed a linear relationship between the two fluorescencechannels, consistent with the observation that the 225-1 can bind bothnucleotide states with comparable affinity (FIG. 28 ). A similar profilewas observed for the scanning mutagenesis library. We then performed ascreen, selecting cells that lay above the limits of the 225-1population in the GTP-selective region (see indicated gate). After tworounds of sorting, we isolated a population that appeared to bindRas.GTP more selectively than the 225-1 parent (FIG. 28 ). Sequencingthis population revealed a single conserved mutation of A30R, near theC-terminus of the peptide. The rationale for this substitution is notevident and will require more detailed structural data of theRas-peptide complex to understand, but as one obvious difference betweenRas.GTP and Ras GDP is the presence of an additional phosphate inRas.GTP, it is tempting to speculate that the arginine may be forming anelectrostatic interaction with this anionic group.

Means of Improving the 225 Peptides. The ultimate goal of this projectis to identify new ways of engaging the Ras effector domain with smallpeptides, and ideally to develop a molecule that is capable ofsuppressing Ras activity in cancer cells. We have used yeast display anddirected evolution to identify peptides which bind with mid-to-lownanomolar affinity to the Ras surface and likely target the effectordomain directly. At present, the 225 (homodimer) peptides do not appearto possess Ras-inhibitory activity when used to treat cancer cells, andthere are a number of possibilities for why this may be the case.Although the peptides do appear to be weakly cell permeable, theintracellular concentration they can achieve may be too low given theiraffinity and/or the cellular abundance of Ras proteins, so it ispossible that improvements in either the permeability of affinity of thepeptides may be required for activity. It is also possible that, onceinside the cell, the 225 peptides are sequestered by non-Ras proteins oraway from the inner leaflet of the plasma membrane, where active Ras islocated. Indeed, preliminary results with FITC-labeled 225 peptidessuggest that they may be predominantly localized to the nucleus, perhapsbecause a portion of the peptides are recognized as nuclear localizationsignals (NLS). The PPII helix of the 225 peptides does bear somesimilarity to an NLS identified in S. pombe that is rich in proline andbasic amino acids, although to our knowledge an equivalent signal inhuman cells has not yet been characterized.² Should this prove to be thecase, it may be possible to weaken such localization by testing mutantsof the PPII helix that remove the arginine residues, e.g. by revertingthem to the amino acids found in aPP. Finally, it is possible that the225 peptides are rapidly degraded upon entry to human cells, causingthem to be cleared before they can exert an effect on Ras signaling.

At present, we are evaluating the activity of the putativedisulfide-stabilized dimers (i.e. Y7C homodimers and S13C/I14E-225-1heterodimers). In principle, these molecules may possess both strongeraffinity and improved stability relative to the 225-1 homodimers, and ifwe obtain encouraging results in vitro, we may test their activity inliving cells. Disulfide bonds are generally not stable in human cells,but nevertheless may contribute towards the stability of the peptide-Rascomplex since it is apparent that they are not strictly required fordimerization and Ras binding. One could also imagine preparing thecorresponding selenocysteine peptides in hopes of obtained non-reduciblevariants, as discussed in Chapter I.

One additional strategy to improve the biological activity of the 225peptides is to target them to the cellular compartment where active Rasproteins are localized; namely, the inner leaflet of the plasmamembrane. One obvious way to achieve this is simply to mimic the Rasproteins and conjugate the peptides to a lipophilic group, such as afarnesyl or hexadecyl moiety. In principle, this should result in theRas proteins experiencing a relatively high local concentration of the225 peptides, which could improve the ability of the 225 peptides tocompete with effectors, which generally are not tethered to themembrane. We conducted initial tests of this strategy with the 225peptides prior to discovering that they act as a dimer, and the negativeresults we obtained are likely a consequence of dimer disruption uponmembrane anchoring (analogous to the inability of biotinylated peptidesto bind Ras when immobilized to a streptavidin SPR chip). If thedisulfide-stabilized dimers prove stable, we will attempt to preparemono-lipidated dimers (using substoichiometric equivalents of labelduring the lipidation reaction) to test whether such peptides are ableto inhibit Ras activity in cells.

Future Directions for the Ras Project. If the peptide-dimer hypothesisis correct, then the size of the Ras-binding 225 species isapproximately 9 kDa. This is rather large compared to thecell-penetrating active peptides discussed in the Introduction, and itwould be preferable for the molecular weight to be significantly lower.We do not currently know which residues on the peptide dimer areinvolved in binding the Ras surface, but it seems likely that they arepredominantly localized on the a-helix, given that this was the peptideface that was randomized for the library (if the 225 peptides engagedRas through the PPII helices, which were the same for all librarymembers, one would not expect a rare and specific a-helical consensus tobe required for binding). Furthermore, the a-helix was the site ofnearly all the mutations that arose during the directed evolution, withthe exception of the cysteine mutants that we hypothesize are involvedin dimer stabilization. If the a-helices do indeed comprise theRas-interacting region of the 225 peptide dimer, then the PPII helicesmay be dispensable, provided that we can identify an alternative meansof stabilizing the dimer. The head-to-tail orientation of the dimermodel suggests a possible solution to this: because the N- and C-terminiof each a-helix are in close proximity, it may be possible to condensethe molecule into a monomer, in which one a-helix is followed by a loop(of yet unknown composition) and then the second a-helix (FIG. 29 ).

In principle, this approach could afford a peptide whose molecularweight is nearly half that of the 225 dimer. One key issue, however, isthe length and composition of the loop between helices. Inspection ofthe aPP dimer suggests that a loop length of 4-6 amino acids may beideal, but the optimal length is difficult to predict, particularlygiven that we do not possess an actual structure of the 225 dimer. Theloop composition is similarly difficult to predict. Fortunately, thisproblem is well suited to yeast surface display: by constructing alibrary with randomized loops of 4-6 amino acids between the two 225α-helices, it should be possible to identify loops that stabilize thetwo helices into a Ras-binding conformation, provided that our model ofthe Ras-peptide interaction is largely correct. We have designed such alibrary (FIG. 29 ), with the added feature of cysteine residues at theN- and C-termini of the construct, to allow for the possibility ofdisulfide bridging across the helices. Because the optimal distancebetween these two residues is also challenging to predict, the librarywas synthesized to allow two different positions for each cysteine (byinserting a glycine residue), with four possible combinations total.Furthermore, because several hydrophobic a-helical residues on the“interior” of the 225 peptide are involved in packing with the PPIIhelix, we either replaced them with alanine or randomized them.

We have prepared this library and plan to begin screening it soon.Should it afford hits, we will perform the same battery of in vitroassays used to characterize the 225 peptides, to determine whether thenew sequences bind the Ras effector domain with reasonable affinity andspecificity. We may then use directed evolution to improve theproperties of the peptides, and will ultimately aim to test theiractivity in cells. As disulfide bonds are not generally stable in humancells, we will need to develop an alternative means of stabilizing thepeptide should our new peptides prove dependent on the disulfide bondsfor activity. One possibility would be to replace the cysteine residueswith selenocysteine. It could also be possible to prepare a head-to-tailbackbone cyclized peptide, either through chemical synthesis or anintein strategy.³ Finally, if the new peptides largely retain anα-helical binding conformation, they may be suitable candidates forall-hydrocarbon stapling. We intend to pursue these avenues if hits fromthe yeast display screens emerge.

Example 5 Covalent Peptide Dimer Formation

A peptide monomer comprising a cysteine (SEQ ID NO: 30) protected witht-butyl and a peptide monomer comprising an acrylamide (SEQ ID NO: 31)were mixed together in 50 mM Tris-Cl pH 8 at a final concentration of 5μM for each peptide. To these samples were added either 1 mM or 10 mMreduced glutathione, and the samples were incubated at room temperaturefor 45 minutes before adding 80 μl of reaction to 10 μl of 1%trifluoroacetic acid and analyzing by LC-MS using a C18 column and a10-100% acetonitrile gradient in water with 0.1% trifluoroacetic acid.

FIGS. 35A-B show a mass chromatogram from an LC-MS analysis of SEQ IDNO: 30 peptide monomer mixed with a SEQ ID NO: 31 peptide monomer,either with a low level of glutathione (1 mM) (FIG. 35A), which cannotreduce the t-butyl thiol protected cysteine effectively), or a higherlevel of glutathione (10 mM) (FIG. 35B), which results in covalentcrosslinking between the peptide of SEQ ID NO: 30 and the peptide of SEQID NO: 31, as seen by the appearence of the indicated ion.

Example 6 Selective Dimer Destabilization

Live-cell confocal microscopy was performed with labeled peptides,performed in H358 lung adenocarcinoma cells, at 5 μM concentration offluorescein-labeled peptide, in DMEM media supplemented with 10% fetalcalf serum. FIG. 36A shows peptides of SEQ ID NO: 37, which lackshistidines. FIG. 36B shows peptides of SEQ ID NO: 38, which contains twohistidines per monomer (four histidines per dimer; “His tetrad”).

Example 7 Dimer Destabilization using Bulky Moieties

FIG. 37 shows a peptide of SEQ ID NO: 42 in which the Cys was reactedwith 2,2′-Dipyridyldisulfide to create a disulfide-protected cysteine.This cysteine is uncaged in the presence of low glutathione levels toform the disulfide-bonded species, which is a better Ras binder. Thefollowing data demonstrate an increase in Ras binding upon addition of 5mM reduced glutathione, which results in the formation of the covalentdisulfide-bonded dimer, as verified by mass spectrometry. Theexperimentals are the similar to those described for FIG. 19 .

Example 8 Peptides Binding to Additional Targets

FIGS. 38A-C shows yeast surface display binding data for peptides of SEQID NO: 43 to 45 with their corresponding protein targets. Experimentalfor yeast display assays were similar to those used for FIG. 9 . MY01peptide of SEQ ID NO: 43 corresponds to the indicated high-bindingpopulation in FIG. 38C. Purification of the RalA protein was similar tothe methods used for KRas constructs as discussed previously.

Purification of the Myc/Max proteins was done as follows. A bicistronicpET vector containing His₆-yBBr-TEV-Myc (residues 353-434) and untaggedMax (residues 22-102) was transformed into chemically competent BL21cells. The cells were grown to OD₆₀₀=0.7, induced with 0.25 mM IPTG for5 hours at 30° C., then harvested and resuspended in lysis buffer (20 mMHEPES pH 7.5, 500 mM KCl, 5% glycerol) prior to snap-freezing in liquidnitrogen. For purification, the pellet was thawed, raised to 40 ml inthe same buffer, and mixed with a Roche Complete EDTA-free proteaseinhibitor tablet. The cells were lysed with a tip sonicator (VirSonic, 6cycles of 10 s on, 15 s off at 6.5 power level), then pelleted at30,000×g for 30 minutes and filtered through a 0.45 uM Tuffryn membrane(Pall Corporation). The clarified lysate was added to 2 ml of HisPurNi-NTA resin (Thermo Pierce) that had been equilibrated with the samebuffer, and drained by gravity. he column was washed with 20 ml ofbuffer, then protein was eluted with buffer containing 150 mM imidazoleand some protease inhibitor. Immediately following elution from thecolumn, EDTA was added to 0.5 mM. The protein was concentrated in aCentriprep YM-10 (Millipore) to 2 ml and gel filtered into 20 mM HEPESpH 7.5, 150 mM KCl, 1 mM EDTA, 5% glycerol using a Superdex 75 column.The protein was labeled with Alexa647 as described for the Ras proteinsabove.

Equivalents and Scope

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process.

Furthermore, the invention encompasses all variations, combinations, andpermutations in which one or more limitations, elements, clauses, anddescriptive terms from one or more of the listed claims is introducedinto another claim. For example, any claim that is dependent on anotherclaim can be modified to include one or more limitations found in anyother claim that is dependent on the same base claim. Where elements arepresented as lists, e.g., in Markush group format, each subgroup of theelements is also disclosed, and any element(s) can be removed from thegroup. It should it be understood that, in general, where the invention,or aspects of the invention, is/are referred to as comprising particularelements and/or features, certain embodiments of the invention oraspects of the invention consist, or consist essentially of, suchelements and/or features. For purposes of simplicity, those embodimentshave not been specifically set forth in haec verba herein. It is alsonoted that the terms “comprising” and “containing” are intended to beopen and permits the inclusion of additional elements or steps. Whereranges are given, endpoints are included. Furthermore, unless otherwiseindicated or otherwise evident from the context and understanding of oneof ordinary skill in the art, values that are expressed as ranges canassume any specific value or sub-range within the stated ranges indifferent embodiments of the invention, to the tenth of the unit of thelower limit of the range, unless the context clearly dictates otherwise.

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference. If there is a conflict between any ofthe incorporated references and the instant specification, thespecification shall control. In addition, any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Because such embodimentsare deemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the invention can be excluded from any claim,for any reason, whether or not related to the existence of prior art.

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present embodimentsdescribed herein is not intended to be limited to the above Description,but rather is as set forth in the appended claims. Those of ordinaryskill in the art will appreciate that various changes and modificationsto this description may be made without departing from the spirit orscope of the present invention, as defined in the following claims.

1. A peptide comprising a sequence of: (SEQ ID NO: 1)X₁PX₃X₄PX₆X₇PGX₁₀X₁₁AX₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅ X₂₆YLKX₂₉X₃₀VA

wherein: X₁ is Gly, Arg, or an amino acid capable of cross-linking thepeptide with another peptide; X₃, X₄, and X₆ are each independently acharged amino acid; X₁₀ is a charged amino acid; X₇ is Tyr or an aminoacid capable of cross-linking the peptide with another peptide; X₁₁ is acharged amino acid or an amino acid capable of cross-linking the peptidewith another peptide; X₁₃ is Ser or an amino acid capable ofcross-linking the peptide with another peptide; X₁₄ is Ile or Glu; X₁₅is Glu, Asp, Gln, or Gly; X₁₈ is an aromatic or hydrophobic amino acid;X₁₉ is Glu, Asp, Gln, Ala, or Trp; X₂₁, X₂₅, X₂₉ are each independentlya Tyr, Phe, Trp, His, or an amino acid with a cyclohexyl side chain,wherein Tyr, Phe, Trp, cylohexyl side chain can be substituted with oneor more fluorines; X₂₂ is Ala, Gly, Ser, or Val; X₂₆ is Asn, Leu, Ile,or His; X₃₀ is Ala or Arg; wherein the peptide comprises one to twoamino acids capable of cross-linking the peptide with another peptide;or a peptide comprising a sequence of:X-₆X-₅X-₄X-₃X-₂X-iX₁PX₃X₄PX₆X₇PGX₁₀X₁₁AX₁₃X₁₄X₁₅X₁₆LX₁₈X₁₉X₂₀X₂₁X₂₂X₂₃LX₂₅X₂₆YLX₂₉X₃₀X₃₁X₃₂ (SEQ ID NO: 13), wherein X₃ and X₄ are each independentlya neutral or charged amino acid; X₆ is a charged amino acid or an aminoacid capable of cross-linking the peptide with another peptide; X₇ isTyr, His, or an amino acid capable of cross-linking the peptide withanother peptide; X₁₀ is Pro, charged amino acid, or an amino acidcapable of cross-linking the peptide with another peptide; X₁₁ is Ala,Ser, neutral or charged amino acid or an amino acid capable ofcross-linking the peptide with another peptide; X₁₃ is Ser, Pro, Thr, oran amino acid capable of cross-linking the peptide with another peptide;X₁₄ is Ile, Glu, Val, Leu, or an amino acid capable of cross-linking thepeptide with another peptide; X₁₅ is Glu, Lys, Arg, Ala, Ser, Asp, Gln,or Gly; X₁₆ is Asp, Glu, Gln, Ala, or Ser; X₁₈ is an aromatic orhydrophobic amino acid; X₁₉ is Glu, Lys, Leu, Met, His, Asp, Gln, Ala,Ser, Trp, or Arg; X₂₀ is Tyr or Phe; X₂₁is Gln, Tyr, Phe, Trp, His, oran amino acid with a cyclohexyl side chain, wherein Tyr, Phe, Trp,cylohexyl side chain can be substituted with one or more fluorines; X₂₂is Ala, Gln, Trp, Leu, Tyr, Gly, Ser, Val, or Asn; X₂₃ is Arg, Asp, Leu,or Ala; X₂₅ is Gln, Tyr, Phe, Trp, His, Asp, or an amino acid with acyclohexyl side chain, wherein Tyr, Phe, Trp, cylohexyl side chain canbe substituted with one or more fluorines; X₂₆ is Asn, Ala, Leu, Arg,Phe, Ile, His, or Gln; X₂₉ is Ala, Leu, Glu, Asn, Gln, Tyr, Phe, Trp,His, or an amino acid with a cyclohexyl side chain, wherein Tyr, Phe,Trp, cylohexyl side chain can be substituted with one or more fluorines;X₃( )is Ala, Arg or Val; X₃₁ is V or an amino acid capable ofcross-linking the peptide with another peptide; X₃₂ is V, Ala, Arg, Ser,or an amino acid capable of cross-linking the peptide with anotherpeptide; X-₆, X-₅, X-₄, X-₃, X-₂, X-₁, and X₁ are optional; and whereinthe peptide comprises one to two amino acids capable of cross-linkingthe peptide with another peptide; or a peptide comprising a sequence of:X₁PX₃X₄PX₆X₇PGX₁₀AAX₁₃X₁₄AALHAYX₂₁AX₂₃LX₂₅NYLX₂₉X₃₀VX₃₂ (SEQ ID NO: 48,wherein X₁ is optionally present and when present, X₁ is Gly, Arg, or anamino acid capable of cross-linking the peptide with another peptide;X₃, X₄ and X₆ are each independently a neutral or positively chargedamino acid; X₇ is Tyr or an amino acid capable of cross-linking thepeptide with another peptide; X₁₀ is Asp or a neutral amino acid; X₁₃ isSer, Thr or an amino acid capable of cross-linking the peptide withanother peptide; X₁₄ is Ile or Leu; X₂₁, X₂₅, X₂₉ are each independentlya Tyr, Phe, Trp, His, or an amino acid with a cyclohexyl side chain,wherein Tyr, Phe, Trp, cylohexyl side chain can be substituted with oneor more fluorines; X₂₃ is Arg, Leu or Ala; X₃₀ is Ala or Arg; X₃₂ isAla, Ser, or Arg; and wherein the peptides comprise one to two aminoacids capable of cross-linking the peptide with another peptide; or apeptide dimer comprising a first peptide associated with a secondpeptide, wherein the first and second peptides each independentlycomprise a peptide sequence of: (SEQ ID NO: 1)X₁PX₃X₄PX₆X₇PGX₁₀X₁₁AX₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅ X₂₆YLKX₂₉X₃₀VA

wherein: X₁ is Gly, Arg, or an amino acid capable of cross-linking thepeptide with another peptide; X₃, X₄, and X₆ are each independently acharged amino acid; X₁₀ is a charged amino acid; X₇ is Tyr or an aminoacid capable of cross-linking the peptide with another peptide; X₁₁ is acharged amino acid or an amino acid capable of cross-linking the peptidewith another peptide; X₁₃ is Ser or an amino acid capable ofcross-linking the peptide with another peptide; X₁₄ is Ile or Glu; X₁₅is Glu, Asp, Gln, or Gly; X₁₈ is an aromatic or hydrophobic amino acid;X₁₉ is Glu, Asp, Gln, Ala, or Trp; X₂₁, X₂₅, X₂₉ are each independentlya Tyr, Phe, Trp, His, or an amino acid with a cyclohexyl side chain,wherein Tyr, Phe, Trp, cylohexyl side chain can be substituted with oneor more fluorines; X₂₂ is Ala, Gly, Ser, or Val; X₂₆ is Asn, Leu, Ile,or His; X₃₀ is Ala or Arg; wherein the first and second peptides eachcomprises one to two amino acids cross-linking the first peptide withthe second peptide.
 2. (canceled)
 3. The peptide of claim 1, wherein ifX-₆ is present, then X-₆ is Gly and X-₅ to X₁ are present; if X-₅ ispresent, then X-₅ is Cys or Sec and X-₄ to X₁ are present; if X-₄ ispresent, then X-₄ is Gly and X-₃ to X₁ are present; if X-₃ is present,then X-₃ is Gly and X-₂ to X₁ are present; if X-₂ is present, then X-₂is Pro, Cys, Sec, or Gly and X-i and X₁ are present; if X-₁ is present,then X-₁ is Arg or Gly and X₁ is present; and if X₁ is present, X₁ isGly, Arg, or an amino acid capable of cross-linking the peptide withanother peptide.
 4. The peptide of claim 3, wherein X-₆ to X₁ are notpresent; X₁₁, X₁₅, X₁₆, X₁₉ are each Ala or Ser; X₁₈ is His; X₂₀ is Tyr,and X₂₆ is Asn. 5-6. (canceled)
 7. A peptide dimer comprising a firstpeptide associated with a second peptide, wherein the first and secondpeptides each independently comprise a peptide sequence of SEQ ID NO: 13of claim
 1. 8. A peptide dimer comprising a first peptide associatedwith a second peptide, wherein the first and second peptides eachindependently comprise a peptide sequence of SEQ ID NO: 48 of claim 5.9. A peptide dimer comprising a first peptide associated with a secondpeptide, wherein the first and second peptides each independentlycomprise a peptide sequence selected from SEQ ID NO: 1, 13, or 48 ofclaim
 1. 10. The peptide dimer of claim 1, wherein the dimer is ahomodimer.
 11. The peptide dimer of claim 1, wherein the dimer is aheterodimer. 12-58. (canceled)
 59. The peptide of claim 1, wherein thepeptide is a first peptide that associates with a second peptide to forma peptide dimer that binds to a target protein, wherein the targetprotein is Ras, a Ras mutant, Myc/Max, RalA, Beta catenin, YAP/TEAD, andNEMO/IκB kinase, 60-78. (canceled)
 79. A peptide comprising aoligomerization domain comprising a sequence of: PX_(a)X_(b)PX_(c)X_(d)P(SEQ ID NO: 2), wherein X_(a), X_(b), X_(c) is any non-proline aminoacid, and X_(d) is an amino acid capable of cross-linking the peptidewith a second peptide, or a peptide comprising a oligomerization domaincomprising a sequence of: PX_(a)X_(b)PX_(c)X_(d)P (SEQ ID NO: 2),wherein X_(a), X_(b) is any non-proline amino acid; and X_(c) and X_(d)is an amino acid capable of cross-linking the peptide with a secondpeptide.
 80. (canceled)
 81. The peptide of claims 79, wherein the secondpeptide comprises a sequence of: PX_(a)X_(b)PX_(c)X_(d)P (SEQ ID NO: 2).82. The peptide of claim 79, further comprising an alpha-helical domaincomprising a sequence of: X₁₃X₁₄X₁₅DLX₁₈X₁₉YX₂₁X₂₂RLX₂₅X₂₆YLX₂₉X₃₀VA(SEQ ID NO: 3), wherein X₁₃, X₁₄, X₁₅, X₁₈, X₁₉, X₂₁, X₂₂, X₂₅, X₂₆,X₂₉, and X₃₀ are as defined in any one of the preceding claims. 83-100.(canceled)
 101. A method of treating a disease or condition associatedwith Ras in a subject in need thereof comprising administering a peptideof claim 1 to the subject.
 102. The method of claim 101, wherein thedisease associated with Ras is a proliferative disease.
 103. The methodof claim 101, wherein the proliferative disease is cancer.
 104. Themethod of claim 101, wherein the disease associated with Ras is CFCsyndrome, capillary malformation-arteriovenous malformation syndrome,Costello syndrome, Legius syndrome, Neurofibromatosis type 1, Noonansyndrome, or Noonan syndrome with multiple lentigines (formerly LEOPARDsyndrome).
 105. A method of screening a library of peptide dimers,comprising the steps of: transforming display cells with a vectorencoding a first peptide and a second peptide, wherein the first andsecond peptides associate to form a peptide dimer fused to a cell wallprotein, contacting the display cells with a first label, wherein thefirst label comprises a target protein and associates with a cellexpressing the peptide dimer having enhanced binding to the target anddoes not associate with a cell which does not express the peptide dimerhaving enhanced binding to the target; isolating the display cells withwhich the first label is associated; and identifying the first andsecond peptides which exhibit enhanced binding to the target.
 106. Themethod of claim 105, wherein the peptide dimer is a peptide homodimer ora peptide heterodimer of two peptides each comprising an alpha-helicalstructure. 107-114. (canceled)
 115. A nucleic acid encoding a peptide ofclaim
 1. 116. A host cell comprising a nucleic acid of claim
 115. 117. Ahost cell comprising a peptide of claim 1.